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Bibliography on: Metagenomics

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ESP: PubMed Auto Bibliography 08 Jul 2020 at 01:31 Created: 


While genomics is the study of DNA extracted from individuals — individual cells, tissues, or organisms — metagenomics is a more recent refinement that analyzes samples of pooled DNA taken from the environment, not from an individual. Like genomics, metagenomic methods have great potential in many areas of biology, but none so much as in providing access to the hitherto invisible world of unculturable microbes, often estimated to comprise 90% or more of bacterial species and, in some ecosystems, the bulk of the biomass. A recent describes how this new science of metagenomics is beginning to reveal the secrets of our microbial world: The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members.

Created with PubMed® Query: metagenomic OR metagenomics OR metagenome NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2020-07-07

Shi X, Gao G, Tian J, et al (2020)

Symbiosis of sulfate-reducing bacteria and methanogenic archaea in sewer systems.

Environment international, 143:105923 pii:S0160-4120(20)31878-X [Epub ahead of print].

Sulfide and methane emissions always simultaneously exist in natural environment and constitute a major topic of societal concern. However, the metabolic environments between sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) exist a great difference, which seems to be opposite to the coexisting phenomenon. To explore this issue, the comprehensive biofilm structures, substrate consuming and metabolism pathways of SRB and MA were investigated in a case study of urban sewers. The results showed that, due to the stricter environmental requirements of MA than SRB, SRB became the preponderant microorganism which promoted the rapid generation of sulfide in the initial period of biofilm formation. According to a metagenomic analysis, the SRB appeared to be more preferential than MA in sewers, and the preponderant SRB could provide a key medium (Methyl-coenzyme M) for methane metabolism. Therefore, the diversity of MA gradually increased, and the symbiosis system formed preliminarily. In addition, via L-cysteine, methane metabolism also participated in sulfide consumption which was involved in cysteine and methionine metabolism. This phenomenon of sulfide consumption led to the forward reaction of sulfide metabolism, which could promote sulfide generation while stabilizing the pH value (H+ concentration) and S2- concentrations which should have inhibited SRB and MA production. Therefore, the heavily intertwined interactions between sulfide and methane metabolism provided environmental security for SRB and MA, and completely formed the symbiosis between SRB and MA. Based on these findings, an ecological model involving synergistic mechanism between sulfide and methane generation is proposed and this model can also improve understanding on the symbiosis of SRB and MA in the natural environment.

RevDate: 2020-07-07

Xiaoting L, Shanshan L, Qiuhong W, et al (2020)

Metagenomics approach the intestinal microbiome structure and function in the anti-H1N1 of a traditional chinese medicine acid polysaccharide.

Microbial pathogenesis pii:S0882-4010(20)30717-8 [Epub ahead of print].

Ephedra sinica Stapf polysaccharide is a pure acidic uniform polysaccharide extracted from the traditional Chinese medicine Ephedra sinica Stapf. In our past research, it was found that it has anti-inflammatory response and suppresses immunity. Therefore, in this experiment, mice were infected with FM1 virus, treated with Ephedra sinica Stapf polysaccharide, and metagene sequencing was used to sequence the mouse intestinal contents. As a result, we found that Ephedra sinica Stapf polysaccharide has obvious therapeutic effect on acute lung injury caused by H1N1. In the intestinal flora, the abundance of Lactobacillales and Bifidobacteriaceae increased significantly, and the metabolome increased significantly in the KEGG pathway. The intestinal flora may be an important target of Ephedra sinica Stapf polysaccharides metabolism against H1N1.

RevDate: 2020-07-07

Kwong WK (2020)

Microbiome Evolution: Having the Guts to Be Different.

Current biology : CB, 30(13):R766-R768.

Metagenomic sequencing of the gut microbial communities of two closely related bee species, the Western honey bee (Apis mellifera) and the Eastern honey bee (Apis cerana), show that organisms with similar characteristics can harbor unexpected differences in their microbiomes.

RevDate: 2020-07-07

Rahman N, Shah M, Muhammad I, et al (2020)

Genome-wide core proteome analysis of Brucella melitensis Strains for Potential Drug Target Prediction.

Mini reviews in medicinal chemistry pii:MRMC-EPUB-107961 [Epub ahead of print].

Brucella melitensis is a facultative intracellular bacterial pathogen that causes abortion in goats and sheep and Malta fever in humans. Human chronic infection is successfully established through contact with infected animals or their dirty product. Subtractive genomic approach is considered as a powerful and useful method for the identification of potential drug and vaccine targets. In this study an attempt has been made through subtractive proteomic strategy to identify novel drug targets in Brucella melitensis strains. There were 2604 core proteins of 56 strains of B. melitensis, of which 545 nonhuman homologs were found to be essential for pathogen growth. Metabolic pathway analysis of these essential proteins revealed that 129 proteins are exclusively involved in 21 unique metabolic pathways in B. melitensis reference strain. Of these, 31 proteins were found to be involved in 10 metabolic pathways which are unique to the pathogen. We selected Nitrate reductase subunit-β, Urease subunit α-2, Pantoate-β-alanine ligase, Isochorismatase, 2-dehydro-3- deoxyphosphooctonate aldolase and Serine O-acetyltransferase as a drug targets in Brucella melitensis strains. Among these druggable targets, we selected only Pantoate-β-alanine ligase as high confidence target based on intensive literature curation, which is non homologous to human gut metagenome involved in Biosynthesis of secondary metabolites pathway. Pantothenate synthetase, it the best chemotherapeutic target to combat Brucellulosis. Further in vitro and in vivo validation is needed for the evaluation of lead compound against Brucella melitensis strains.

RevDate: 2020-07-07

Tovo A, Menzel P, Krogh A, et al (2020)

Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju.

Nucleic acids research pii:5868338 [Epub ahead of print].

Characterizing species diversity and composition of bacteria hosted by biota is revolutionizing our understanding of the role of symbiotic interactions in ecosystems. Determining microbiomes diversity implies the assignment of individual reads to taxa by comparison to reference databases. Although computational methods aimed at identifying the microbe(s) taxa are available, it is well known that inferences using different methods can vary widely depending on various biases. In this study, we first apply and compare different bioinformatics methods based on 16S ribosomal RNA gene and shotgun sequencing to three mock communities of bacteria, of which the compositions are known. We show that none of these methods can infer both the true number of taxa and their abundances. We thus propose a novel approach, named Core-Kaiju, which combines the power of shotgun metagenomics data with a more focused marker gene classification method similar to 16S, but based on emergent statistics of core protein domain families. We thus test the proposed method on various mock communities and we show that Core-Kaiju reliably predicts both number of taxa and abundances. Finally, we apply our method on human gut samples, showing how Core-Kaiju may give more accurate ecological characterization and a fresh view on real microbiomes.

RevDate: 2020-07-07

Mu A, Thomas BC, Banfield JF, et al (2020)

Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph.

Environmental microbiology reports [Epub ahead of print].

Microbial communities play important roles in the biogeochemical cycling of carbon in the Earth's deep subsurface. Previously, we demonstrated changes to the microbial community structure of a deep aquifer (1.4 km) receiving 150 tons of injected supercritical CO2 (scCO2) in a geosequestration experiment. The observed changes support a key role in the aquifer microbiome for the thermophilic CO-utilising anaerobe Carboxydocella, which decreased in relative abundance post-scCO2 injection. Here, we present results from more detailed metagenomic profiling of this experiment, with genome resolution of the native carboxydotrophic Carboxydocella. We demonstrate a switch in CO-oxidation potential by Carboxydocella through analysis of its carbon monoxide dehydrogenase (CODH) gene before and after the geosequestration experiment. We discuss the potential impacts of scCO2 on subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide (CO). This article is protected by copyright. All rights reserved.

RevDate: 2020-07-07

Meijnikman AS, Aydin O, Prodan A, et al (2020)

Distinct differences in gut microbial composition and functional potential from lean to morbidly obese subjects.

Journal of internal medicine [Epub ahead of print].

INTRODUCTION: The gut microbiome may contribute to the development of obesity. So far, the extent of microbiome variation in people with obesity has not been determined in large cohorts and for a wide range of body mass index (BMI). Here, we aimed to investigate whether the faecal microbial metagenome can explain the variance in several clinical phenotypes associated with morbid obesity.

METHODS: Caucasian subjects were recruited at our hospital. Blood pressure and anthropometric measurements were taken. Dietary intake was determined using questionnaires. Shotgun metagenomic sequencing was performed on faecal samples from 177 subjects.

RESULTS: Subjects without obesity (n = 82, BMI 24.7 ± 2.9 kg m-2) and subjects with obesity (n = 95, BMI 38.6 ± 5.1 kg m-2) could be clearly distinguished based on microbial composition and microbial metabolic pathways. A total number of 52 bacterial species differed significantly in people with and without obesity. Independent of dietary intake, we found that microbial pathways involved in biosynthesis of amino acids were enriched in subjects with obesity, whereas pathways involved in the degradation of amino acids were depleted. Machine learning models showed that more than half of the variance in body fat composition followed by BMI could be explained by the gut microbiome composition and microbial metabolic pathways, compared to 6% of variation explained in triglycerides and 9% in HDL.

CONCLUSION: Based on the faecal microbiota composition, we were able to separate subjects with and without obesity. In addition, we found strong associations between gut microbial amino acid metabolism and specific microbial species in relation to clinical features of obesity.

RevDate: 2020-07-07

Chng KR, Ghosh TS, Tan YH, et al (2020)

Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut.

Nature ecology & evolution pii:10.1038/s41559-020-1236-0 [Epub ahead of print].

Loss of diversity in the gut microbiome can persist for extended periods after antibiotic treatment, impacting microbiome function, antimicrobial resistance and probably host health. Despite widespread antibiotic use, our understanding of the species and metabolic functions contributing to gut microbiome recovery is limited. Using data from 4 discovery cohorts in 3 continents comprising >500 microbiome profiles from 117 individuals, we identified 21 bacterial species exhibiting robust association with ecological recovery post antibiotic therapy. Functional and growth-rate analysis showed that recovery is supported by enrichment in specific carbohydrate-degradation and energy-production pathways. Association rule mining on 782 microbiome profiles from the MEDUSA database enabled reconstruction of the gut microbial 'food web', identifying many recovery-associated bacteria as keystone species, with the ability to use host- and diet-derived energy sources, and support repopulation of other gut species. Experiments in a mouse model recapitulated the ability of recovery-associated bacteria (Bacteroides thetaiotaomicron and Bifidobacterium adolescentis) to promote recovery with synergistic effects, providing a boost of two orders of magnitude to microbial abundance in early time points and faster maturation of microbial diversity. The identification of specific species and metabolic functions promoting recovery opens up opportunities for rationally determining pre- and probiotic formulations offering protection from long-term consequences of frequent antibiotic usage.

RevDate: 2020-07-07

Keohane DM, Ghosh TS, Jeffery IB, et al (2020)

Microbiome and health implications for ethnic minorities after enforced lifestyle changes.

Nature medicine pii:10.1038/s41591-020-0963-8 [Epub ahead of print].

Modern lifestyles increase the risk of chronic diseases, in part by modifying the microbiome, but the health effects of lifestyles enforced on ethnic minorities are understudied1-3. Lifestyle affects the microbiome early in life, when the microbiome is assembled and the immune system is undergoing maturation4-6. Moreover, the influence of lifestyle has been separated from genetic and geographic factors by studies of genetically similar populations and ethnically distinct groups living in the same geographic location7-11. The lifestyle of Irish Travellers, an ethnically distinct subpopulation, changed with legislation in 2002 that effectively ended nomadism and altered their living conditions. Comparative metagenomics of gut microbiomes shows that Irish Travellers retain a microbiota similar to that of non-industrialized societies. Their microbiota is associated with non-dietary factors and is proportionately linked with risk of microbiome-related metabolic disease. Our findings suggest there are microbiome-related public health implications when ethnic minorities are pressured to change lifestyles.

RevDate: 2020-07-07

Nelson MT, Wolter DJ, Eng A, et al (2020)

Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome.

Thorax pii:thoraxjnl-2019-214187 [Epub ahead of print].

RATIONALE: The most common antibiotic used to treat people with cystic fibrosis (PWCF) is inhaled tobramycin, administered as maintenance therapy for chronic Pseudomonas aeruginosa lung infections. While the effects of inhaled tobramycin on P. aeruginosa abundance and lung function diminish with continued therapy, this maintenance treatment is known to improve long-term outcomes, underscoring how little is known about why antibiotics work in CF infections, what their effects are on complex CF sputum microbiomes and how to improve these treatments.

OBJECTIVES: To rigorously define the effect of maintenance tobramycin on CF sputum microbiome characteristics.

METHODS AND MEASUREMENTS: We collected sputum from 30 PWCF at standardised times before, during and after a single month-long course of maintenance inhaled tobramycin. We used traditional culture, quantitative PCR and metagenomic sequencing to define the dynamic effects of this treatment on sputum microbiomes, including abundance changes in both clinically targeted and untargeted bacteria, as well as functional gene categories.

MAIN RESULTS: CF sputum microbiota changed most markedly by 1 week of antibiotic therapy and plateaued thereafter, and this shift was largely driven by changes in non-dominant taxa. The genetically conferred functional capacities (ie, metagenomes) of subjects' sputum communities changed little with antibiotic perturbation, despite taxonomic shifts, suggesting functional redundancy within the CF sputum microbiome.

CONCLUSIONS: Maintenance treatment with inhaled tobramycin, an antibiotic with demonstrated long-term mortality benefit, primarily impacted clinically untargeted bacteria in CF sputum, highlighting the importance of monitoring the non-canonical effects of antibiotics and other treatments to accurately define and improve their clinical impact.

RevDate: 2020-07-07

Zou D, Wan R, Han L, et al (2020)

Genomic Characteristics of a Novel Species of Ammonia-oxidizing Archaea from the Jiulong River Estuary.

Applied and environmental microbiology pii:AEM.00736-20 [Epub ahead of print].

Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems, and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we have described the AOA communities along the Jiulong River Estuary in Southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, Ca Nitrosopumilus aestuariumsis sp. nov., based on the phylogenies of the 16S-23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy metal-contaminated Jiulong River Estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlights AOA contribution to ammonia oxidation in the Jiulong River Estuary.IMPORTANCE In this study, AOA communities along a river of Southern China were characterized and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, this study suggested adaptation of the novel AOAs to estuarine environments, providing new information for ecology of estuarine AOA and nitrogen cycle in contaminated estuarine environments.

RevDate: 2020-07-07

Brown CT, Moritz D, O'Brien MP, et al (2020)

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity.

Genome biology, 21(1):164 pii:10.1186/s13059-020-02066-4.

Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome. We apply this system to recover missing content from genome bins and show that substantial genomic sequence variation is present in a real metagenome. Our software implementation is available at under the 3-Clause BSD License.

RevDate: 2020-07-07

Williams SH, Levy A, Yates RA, et al (2020)

The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia.

Viruses, 12(7): pii:v12070717.

Metagenomics revealed an impressive breadth of previously unrecognized viruses. Here, we report the virome of the Culex annulirostris Skuse mosquito, an important vector of pathogenic arboviruses in Australia. Mosquitoes were collected from three sites in the Kimberley region of Western Australia. Unbiased high-throughput sequencing (HTS) revealed the presence of 16 novel viral sequences that share less than 90% identity with known viruses. None were closely related to pathogenic arboviruses. Viruses were distributed unevenly across sites, indicating a heterogeneous Cx. annulirostris virome. Polymerase chain reaction assays confirmed HTS data and identified marked variation between the virus prevalence identified at each site.

RevDate: 2020-07-07

Lagos L, Leanti La Rosa S, Ø Arntzen M, et al (2020)

Isolation and Characterization of Extracellular Vesicles Secreted In Vitro by Porcine Microbiota.

Microorganisms, 8(7): pii:microorganisms8070983.

The secretion of extracellular vesicles, EVs, is a common process in both prokaryotic and eukaryotic cells for intercellular communication, survival, and pathogenesis. Previous studies have illustrated the presence of EVs in supernatants from pure cultures of bacteria, including Gram-positive and Gram-negative glycan-degrading gut commensals. However, the isolation and characterization of EVs secreted by a complex microbial community have not been clearly reported. In a recent paper, we showed that wood-derived, complex β-mannan, which shares a structural similarity with conventional dietary fibers, can be used to modulate the porcine gut microbiota composition and activity. In this paper, we investigated the production, size, composition, and proteome of EVs secreted by pig fecal microbiota after 24 h enrichment on complex β-mannan. Using transmission electron microscopy and nanoparticle tracking analysis, we identified EVs with an average size of 165 nm. We utilized mass spectrometry-based metaproteomic profiling of EV proteins against a database of 355 metagenome-assembled genomes (MAGs) from the porcine colon and thereby identified 303 proteins. For EVs isolated from the culture grown on β-mannan, most proteins mapped to two MAGs, MAG53 and MAG272, belonging to the orders Clostridiales and Bacilli, respectively. Furthermore, the MAG with the third-most-detected protein was MAG 343, belonging to the order Enterobacteriales. The most abundant proteins detected in the β-mannan EVs proteome were involved in translation, energy production, amino acid, and carbohydrate transport, as well as metabolism. Overall, this proof-of-concept study demonstrates the successful isolation of EVs released from a complex microbial community; furthermore, the protein content of the EVs reflects the response of specific microbes to the available carbohydrate source.

RevDate: 2020-07-07

Host institution: Department of Food Hygiene and Technology, Institute of Food Science and Technology, Universidad de León, León, Spain, Likotrafiti E, Oniciuc EA, et al (2018)

Risk assessment of antimicrobial resistance along the food chain through culture-independent methodologies.

EFSA journal. European Food Safety Authority, 16(Suppl 1):e160811.

Antimicrobial resistance (AMR) represents a major challenge for Public Health and the scientific community, and requires immediate and drastic solutions. Acquired resistance to certain antimicrobials is already widespread to such an extent that their efficacy in the treatment of certain life-threatening infections is already compromised. To date, the emergence and spread of AMR has been attributed to the use, misuse or indiscriminate use of antibiotics as therapeutic drugs in human, animal and plant health, or as growth promoters in veterinary husbandry. In addition, there is growing concern over the possibility of AMR transmission via the food chain. Food processing environments could act as potential hotspots for AMR acquisition and spread. Indeed, biocide use and exposure to food-related stresses and food processing technologies could presumably act as selection pressures for increased microbial resistance against clinically relevant antibiotics. Global AMR surveillance is critical for providing the necessary information to form global strategies and to monitor the effectiveness of public health interventions as well as to detect new trends and emerging threats. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterisation of the strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence and spread of AMR genes. Whole genome sequencing (WGS) of bacterial pathogens is a powerful tool that can be used for epidemiological surveillance, outbreak detection and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on the occurrence of AMR genes. Both approaches can be used to provide the information necessary for the implementation of quantitative risk assessment of AMR transmission routes along the food chain.

RevDate: 2020-07-07
CmpDate: 2020-07-07

Timpano EK, Scheible MKR, KA Meiklejohn (2020)

Optimization of the second internal transcribed spacer (ITS2) for characterizing land plants from soil.

PloS one, 15(4):e0231436.

Molecular-based taxonomy, specifically DNA barcoding, has streamlined organism identification. For land plants, the recommended 2-locus barcode of rbcL and matK is not suitable for all groups, thus the second subunit of the nuclear internal transcribed spacer (ITS2) has received attention as a possible alternative. To date, evaluations of ITS2 have mostly been limited in scope to specific plant orders/families and single source material. Prior to using ITS2 to routinely characterize land plants present in environmental samples (i.e., DNA metabarcoding), a wet lab protocol optimized for bulk sample types is needed. To address this gap, in this study we determined the broad recoverability across land plants when using published ITS2 primer pairs, and subsequently optimized the PCR reaction constituents and cycling conditions for the best two performing primer pairs (ITS2F/ITSp4 and ITSp3/ITSu4). Using these conditions, both primer pairs were used to characterize land plants present in 17 diverse soils collected from across the US. The resulting PCR amplicons were prepared into libraries and pooled for sequencing on an Illumina® MiniSeq. Our existing bioinformatics workflow was used to process raw sequencing data and taxonomically assign unique ITS2 plant sequences by comparison to GenBank. Given strict quality criteria were imposed on sequences for inclusion in data analysis, only 43.6% and 7.5% of sequences from ITS2F/ITSp4 and ITSp3/ITSu4 respectively remained for taxonomic comparisons; ~7-11% of sequences originated from fungal co-amplification. The number of orders and families recovered did differ between primer pairs, with ITS2F/ITSp4 consistently outperforming ITSp3/ITSu4 by >15%. Primer pair bias was observed in the recovery of certain taxonomic groups; ITS2F/ITSp4 preferentially recovered flowering plants and grasses, whereas ITSp3/ITSu4 recovered more moss taxa. To maximize data recovery and reduce potential bias, we advocate that studies using ITS2 to characterize land plants from environmental samples such as soil use a multiple primer pair approach.

RevDate: 2020-07-06

Yang J, Howe A, Lee J, et al (2020)

An improved approach to identify bacterial pathogens to human in environmental metagenome.

Journal of microbiology and biotechnology pii:jmb.2005.05033 [Epub ahead of print].

The identification of bacterial pathogens to humans is critical for environmental microbial risk assessment. However, current methods for identifying pathogens in environmental samples are limited in their ability to detect highly diverse bacterial communities and accurately differentiate pathogens from commensal bacteria. In the present study, we suggest an improved approach using a combination of identification results obtained from multiple databases, including the multilocus sequence typing (MLST) database, virulence factor database (VFDB), and pathosystems resource integration center (PATRIC) databases to resolve current challenges. By integrating the identification results from multiple databases, potential bacterial pathogens in metagenomes were identified and classified into eight different groups. Based on the distribution of genes in each group, we proposed an equation to calculate the metagenomic pathogen identification index (MPII) of each metagenome based on the weighted abundance of identified sequences in each database. We found that the accuracy of pathogen identification was improved by using combinations of multiple databases compared to that of individual databases. When the approach was applied to environmental metagenomes, metagenomes associated with activated sludge were estimated with higher MPII than other environments (i.e., drinking water, ocean water, ocean sediment, and freshwater sediment). The calculated MPII values were statistically distinguishable among different environments (p<0.05). These results demonstrate that the suggested approach allows more for more accurate identification of the pathogens associated with metagenomes.

RevDate: 2020-07-06

Zheng X, Liu W, Dai X, et al (2020)

Extraordinary diversity of viruses in deep-sea sediments as revealed by metagenomics without prior virion separation.

Environmental microbiology [Epub ahead of print].

Our current knowledge of the virosphere in deep-sea sediments remains rudimentary. Here we investigated viral diversity at both gene and genomic levels in deep-sea sediments of Southwest Indian Ocean. Analysis of 19,676,106 non-redundant genes from the metagenomic DNA sequences revealed a large number of unclassified viral groups in these samples. A total of 1,106 high-confidence viral contigs were obtained after two runs of assemblies, and 217 of these contigs with sizes up to ~120 kb were shown to represent complete viral genomes. These contigs are clustered with no known viral genomes, and over 2/3 of the ORFs on the viral contigs encode no known functions. Furthermore, most of the complete viral contigs show limited similarity to known viral genomes in genome organization. Most of the classified viral contigs are derived from dsDNA viruses belonging to the order Caudovirales, including primarily members of the families Myoviridae, Podoviridae and Siphoviridae. Most of these viruses infect Proteobacteria and, less frequently, Planctomycetes, Firmicutes, Chloroflexi, etc. Auxiliary metabolic genes (AMGs), present in abundance on the viral contigs, appear to function in modulating the host ability to sense environmental gradients and community changes, and to uptake and metabolize nutrients. This article is protected by copyright. All rights reserved.

RevDate: 2020-07-06

Wang W, Ren J, Tang K, et al (2020)

A network-based integrated framework for predicting virus-prokaryote interactions.

NAR genomics and bioinformatics, 2(2):lqaa044.

Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus-prokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures ([Formula: see text] and WIsH). Evaluation of this method on a benchmark set of 1462 known virus-prokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16-27% and 6-10% improvement, respectively, over previous single-feature prediction approaches. We applied our host prediction tool to crAssphage, a human gut phage, and two metagenomic virus datasets: marine viruses and viral contigs recovered from globally distributed, diverse habitats. Host predictions were frequently consistent with those of previous studies, but more importantly, this new tool made many more confident predictions than previous tools, up to nearly 3-fold more (n > 27 000), greatly expanding the diversity of known virus-host interactions.

RevDate: 2020-07-06

EFSA Panel on Biological Hazards (EFSA BIOHAZ Panel), Koutsoumanis K, Allende A, et al (2019)

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms.

EFSA journal. European Food Safety Authority, 17(12):e05898 pii:EFS25898.

This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne pathogens. WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and source-attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial-temporal factors and the detection of multidirectional transmission and pathogen-host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non-culturable, difficult-to-culture or slow-growing microorganisms, for tracking of hazard-related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin-producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS-based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross-border outbreaks and for the development of international standardised risk assessments of food-borne microorganisms.

RevDate: 2020-07-06

Guinot F, Szafranski M, Chiquet J, et al (2020)

Fast computation of genome-metagenome interaction effects.

Algorithms for molecular biology : AMB, 15:13 pii:173.

Motivation: Association studies have been widely used to search for associations between common genetic variants observations and a given phenotype. However, it is now generally accepted that genes and environment must be examined jointly when estimating phenotypic variance. In this work we consider two types of biological markers: genotypic markers, which characterize an observation in terms of inherited genetic information, and metagenomic marker which are related to the environment. Both types of markers are available in their millions and can be used to characterize any observation uniquely.

Objective: Our focus is on detecting interactions between groups of genetic and metagenomic markers in order to gain a better understanding of the complex relationship between environment and genome in the expression of a given phenotype.

Contributions: We propose a novel approach for efficiently detecting interactions between complementary datasets in a high-dimensional setting with a reduced computational cost. The method, named SICOMORE, reduces the dimension of the search space by selecting a subset of supervariables in the two complementary datasets. These supervariables are given by a weighted group structure defined on sets of variables at different scales. A Lasso selection is then applied on each type of supervariable to obtain a subset of potential interactions that will be explored via linear model testing.

Results: We compare SICOMORE with other approaches in simulations, with varying sample sizes, noise, and numbers of true interactions. SICOMORE exhibits convincing results in terms of recall, as well as competitive performances with respect to running time. The method is also used to detect interaction between genomic markers in Medicago truncatula and metagenomic markers in its rhizosphere bacterial community.

Software availability: An R package is available [4], along with its documentation and associated scripts, allowing the reader to reproduce the results presented in the paper.

RevDate: 2020-07-06

Quiroga R, Nistal E, Estébanez B, et al (2020)

Exercise training modulates the gut microbiota profile and impairs inflammatory signaling pathways in obese children.

Experimental & molecular medicine pii:10.1038/s12276-020-0459-0 [Epub ahead of print].

Childhood obesity has reached epidemic levels and is a serious health concern associated with metabolic syndrome, nonalcoholic fatty liver disease, and gut microbiota alterations. Physical exercise is known to counteract obesity progression and modulate the gut microbiota composition. This study aims to determine the effect of a 12-week strength and endurance combined training program on gut microbiota and inflammation in obese pediatric patients. Thirty-nine obese children were assigned randomly to the control or training group. Anthropometric and biochemical parameters, muscular strength, and inflammatory signaling pathways in mononuclear cells were evaluated. Bacterial composition and functionality were determined by massive sequencing and metabolomic analysis. Exercise reduced plasma glucose levels and increased dynamic strength in the upper and lower extremities compared with the obese control group. Metagenomic analysis revealed a bacterial composition associated with obesity, showing changes at the phylum, class, and genus levels. Exercise counteracted this profile, significantly reducing the Proteobacteria phylum and Gammaproteobacteria class. Moreover, physical activity tended to increase some genera, such as Blautia, Dialister, and Roseburia, leading to a microbiota profile similar to that of healthy children. Metabolomic analysis revealed changes in short-chain fatty acids, branched-chain amino acids, and several sugars in response to exercise, in correlation with a specific microbiota profile. Finally, the training protocol significantly inhibited the activation of the obesity-associated NLRP3 signaling pathway. Our data suggest the existence of an obesity-related deleterious microbiota profile that is positively modified by physical activity intervention. Exercise training could be considered an efficient nonpharmacological therapy, reducing inflammatory signaling pathways induced by obesity in children via microbiota modulation.

RevDate: 2020-07-06
CmpDate: 2020-07-06

Garrison NA, Barton KS, Porter KM, et al (2019)

Access and Management: Indigenous Perspectives on Genomic Data Sharing.

Ethnicity & disease, 29(Suppl 3):659-668.

As genomic researchers are encouraged to engage in broad genomic data sharing, American Indian/Alaska Native/Native Hawaiian (AI/AN/NH) leaders have raised questions about ownership of data and biospecimens and concerns over emerging challenges and potential threats to tribal sovereignty. Using a community-engaged research approach, we conducted 42 semi-structured interviews with tribal leaders, clinicians, researchers, policy makers, and tribal research review board members about their perspectives on ethical issues related to genetics in AI/AN/NH communities. We report findings related to perspectives on genetic research, data sharing, and envisioning stronger oversight and management of data. In particular, participants voiced concerns about different models of data sharing, infrastructure and logistics for housing data, and who should have authority to grant access to data. The results will ultimately guide policy-making and the creation of guidelines and new strategies for tribes to drive the research agenda and promote ethically and culturally appropriate research.

RevDate: 2020-07-05

Wang TY, Zhang XQ, Chen AL, et al (2020)

A comparative study of microbial community and functions of type 2 diabetes mellitus patients with obesity and healthy people.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10689-7 [Epub ahead of print].

The gut microbiota is crucial in the pathogenesis of type 2 diabetes mellitus (T2DM). However, the metabolism of T2DM patients is not well-understood. We aimed to identify the differences on composition and function of gut microbiota between T2DM patients with obesity and healthy people. In this study, 6 T2DM patients with obesity and 6 healthy volunteers were recruited, and metagenomic approach and bioinformatics analysis methods were used to understand the composition of the gut microbiota and the metabolic network. We found a decrease in the abundance of Firmicutes, Oribacterium, and Paenibacillus; this may be attributed to a possible mechanism and biological basis of T2DM; moreover, we identified three critical bacterial taxa, Bacteroides plebeius, Phascolarctobacterium sp. CAG207, and the order Acidaminococcales that can potentially be used for T2DM treatment. We also revealed the composition of the microbiota through functional annotation based on multiple databases and found that carbohydrate metabolism contributed greatly to the pathogenesis of T2DM. This study helps in elucidating the different metabolic roles of microbes in T2DM patients with obesity.

RevDate: 2020-07-05

Li J, Liang Y, Miao Y, et al (2020)

Metagenomic insights into aniline effects on microbial community and biological sulfate reduction pathways during anaerobic treatment of high-sulfate wastewater.

The Science of the total environment, 742:140537 pii:S0048-9697(20)34059-6 [Epub ahead of print].

For comprehensive insights into the change of sulfate reduction pathway responding to the toxic stress and the shift of microbial community and performance of sulfate reduction, we built a laboratory-scale expanded granular sludge bed reactor (EGSB) treating high-sulfate wastewater with elevated aniline concentrations from 0 to 480 mg/L. High-throughput sequencing and metagenomic approaches were applied to decipher the molecular mechanisms of sulfate reduction under aniline stress through taxonomic and functional profiles. The increasing aniline in the anaerobic system induced the accumulation of volatile fatty acids (VFA), further turned the bioreactor into acidification, which was the principal reason for the deterioration of system performance and finally resulted in the accumulation of toxic free sulfide. Moreover, aniline triggered the change of bacterial community and genes relating to sulfate reduction pathways. The increase of aniline from 0 to 320 mg/L enriched total sulfate-reducing bacteria (SRB), and the most abundant genus was Desulfomicrobium, accounting for 66.85-91.25% of total SRB. The assimilatory sulfate reduction pathway was obviously inhibited when aniline was over 160 mg/L, while genes associated with dissimilatory sulfate reduction pathways all exhibited an upward tendency with the increasing aniline content. The enrichment of aniline-resistant SRB (e.g. Desulfomicrobium) carrying genes associated with the dissimilatory sulfate reduction pathway also confirmed the underlying mechanism that sulfate reduction turned into dissimilation under high aniline condition. Taken together, these results comprehensively provided solid evidence for the effects of aniline on the biological sulfate reduction processes treating high-sulfate wastewater and the underlying molecular mechanisms which may highlight the important roles of SRB and related sulfate reduction genes during treatment.

RevDate: 2020-07-05

Pei Y, Tao C, Ling Z, et al (2020)

Exploring novel Cr(VI) remediation genes for Cr(VI)-contaminated industrial wastewater treatment by comparative metatranscriptomics and metagenomics.

The Science of the total environment, 742:140435 pii:S0048-9697(20)33957-7 [Epub ahead of print].

Microbial remediation is a promising method to treat Cr(VI) in industrial wastewater. The remediation efficiency and stress-resistance ability of Cr(VI) remediation genes in microbes are the limiting factors for their application in industrial wastewater treatment. To screen novel highly efficient Cr(VI) remediation genes, comparative metatranscriptomic and metagenomic analyses were performed on long-term Cr(VI)-contaminated riparian soil with/without additional Cr(VI) treatment. The most suitable Cr(VI) treatment time was determined to be 30 min according to the high quality RNA yield and fold changes in gene expression. Six novel genes, which had complete open reading frames (ORFs) in metagenomic libraries, were identified from unculturable microbes. In the phenotypic functional assay, all novel genes enhanced the Cr(VI) resistance/reduction ability of E. coli. In the industrial wastewater treatment, E-mcr and E-gsr presented at least 50% Cr(VI) removal efficiencies in the presence of 200-600 μM of Cr(VI), without a decrease in efficiency over 17 days. The stress resistance assay showed that gsr increased the growth rate of E. coli by at least 30% under different extreme conditions, and thus, gsr was identified as a general stress-response gene. In the Cr valence distribution assay, E-mcr presented ~40 μM higher extracellular Cr (III) compared to E-yieF. Additionally, transmission electron microscopy (TEM) of E-mcr showed bulk black agglomerates on the cell surface. Thus, mcr was identified as a membrane chromate reductase gene. This research provides a new idea for studying novel highly efficient contaminant remediation genes from unculturable microbes.

RevDate: 2020-07-05

Bezerra RS, Bitencourt HT, Covas DT, et al (2020)


International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases pii:S1201-9712(20)30531-2 [Epub ahead of print].

OBJECTIVES: Metagenomic analysis of blood units originating from the Brazilian Amazon and positive for parenterally transmitted infections (HIV, HBV, HCV, HTLV, Chagas disease or syphilis).

METHODS: Twenty plasma samples (35% HBV-positive, 10%HIV-positive, 10% HCV-positive, 20% positive for syphilis, 20% for Chagas disease and 5% for HTLV) assembled in pools were analyzed by metagenomic next generation sequencing. The obtained raw sequencing data were submitted to a bioinformatic pipeline set up for identification of emerging viruses. The viral reads of interested were analyzed phylogenetically and confirmed by PCR in the individual samples.

RESULTS: The metagenomic analysis identified contigs belonging to the emerging Human Gemykibivirus-2 (HuGkV-2) in two pools. The performed HuGkV-1 phylogeny demonstrated that the Amazonian isolate formed a separate cluster with other HuGkV-2 strains obtained from human hosts. The PCR confirmation detected HuGkV-1 DNA in 3 individual samples (15%).

CONCLUSIONS: HuGkV-2 is an emerging virus with unknown clinical impact. The detection of HuGkV-2 DNA in blood donations positive for parenterally transmitted infections shows that HuGkV-2 can be considered as an opportunistic viral agent with hypothetic parenteral transmission route.

RevDate: 2020-07-05

Khan Mirzaei M, Xue J, Costa R, et al (2020)

Challenges of Studying the Human Virome - Relevant Emerging Technologies.

Trends in microbiology pii:S0966-842X(20)30162-1 [Epub ahead of print].

In this review we provide an overview of current challenges and advances in bacteriophage research within the growing field of viromics. In particular, we discuss, from a human virome study perspective, the current and emerging technologies available, their limitations in terms of de novo discoveries, and possible solutions to overcome present experimental and computational biases associated with low abundance of viral DNA or RNA. We summarize recent breakthroughs in metagenomics assembling tools and single-cell analysis, which have the potential to increase our understanding of phage biology, diversity, and interactions with both the microbial community and the human body. We expect that these recent and future advances in the field of viromics will have a strong impact on how we develop phage-based therapeutic approaches.

RevDate: 2020-07-04

Ramos RT, Sodré CS, de Sousa Rodrigues PMGR, et al (2020)

High-throughput nucleotide sequencing for bacteriome studies in oral squamous cell carcinoma: a systematic review.

Oral and maxillofacial surgery pii:10.1007/s10006-020-00873-4 [Epub ahead of print].

PURPOSE: Dysbiosis has been identified in oral squamous cell carcinoma (OSCC). The aim of this study was to carry out a systematic review of an electronic research that was carried out on articles published between January 2008 and September 2018.

METHODS: Eight studies were selected after applying the inclusion and exclusion criteria.

RESULTS: All articles targeted the hypervariable regions of the 16S rRNA gene. At the phylum level, it was found reduction of Bacteroidetes (2/8 studies) and increase of Firmicutes (2/8 studies). At the genus level, Rothia increased (1/8 studies) and decreased (2/8 studies) in tumor samples, and Streptococcus also was found increased (3/8 studies) and reduced (3/8 studies). Fusobacterium only increased in OSCC samples (3/8 studies). At species level, an increase in F. nucleatum subsp. polymorphum was more associated to OSCC (2/8 studies) than with controls, as was P. aeruginosa (3/8 studies).

CONCLUSION: In summary, the results corroborated dysbiosis in OSCC patients, with enrichment of microbial taxa that are associated with inflammation and production of acetaldehyde. However, variations of study design and sample size were observed among the studies, as well as a shortage of more detailed analyses of possible correlations between risk habits and OSCC. This lack of more detailed analysis may be the cause of the inconsistencies in regard of the alterations reported for certain genera and species. In conclusion, there is an association between OSCC and oral microbiota dysbiosis, but its role in oral carcinogenesis needs to be clarified in more detail.

RevDate: 2020-07-04

Dyksma S, Jansen L, C Gallert (2020)

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste.

Microbiome, 8(1):105 pii:10.1186/s40168-020-00862-5.

BACKGROUND: Anaerobic digestion (AD) is a globally important technology for effective waste and wastewater management. In AD, microorganisms interact in a complex food web for the production of biogas. Here, acetoclastic methanogens and syntrophic acetate-oxidizing bacteria (SAOB) compete for acetate, a major intermediate in the mineralization of organic matter. Although evidence is emerging that syntrophic acetate oxidation is an important pathway for methane production, knowledge about the SAOB is still very limited.

RESULTS: A metabolic reconstruction of metagenome-assembled genomes (MAGs) from a thermophilic solid state biowaste digester covered the basic functions of the biogas microbial community. Firmicutes was the most abundant phylum in the metagenome (53%) harboring species that take place in various functions ranging from the hydrolysis of polymers to syntrophic acetate oxidation. The Wood-Ljungdahl pathway for syntrophic acetate oxidation and corresponding genes for energy conservation were identified in a Dethiobacteraceae MAG that is phylogenetically related to known SAOB. 16S rRNA gene amplicon sequencing and enrichment cultivation consistently identified the uncultured Dethiobacteraceae together with Syntrophaceticus, Tepidanaerobacter, and unclassified Clostridia as members of a potential acetate-oxidizing core community in nine full-scare digesters, whereas acetoclastic methanogens were barely detected.

CONCLUSIONS: Results presented here provide new insights into a remarkable anaerobic digestion ecosystem where acetate catabolism is mainly realized by Bacteria. Metagenomics and enrichment cultivation revealed a core community of diverse and novel uncultured acetate-oxidizing bacteria and point to a particular niche for them in dry fermentation of biowaste. Their genomic repertoire suggests metabolic plasticity besides the potential for syntrophic acetate oxidation. Video Abstract.

RevDate: 2020-07-04

Creswell R, Tan J, Leff JW, et al (2020)

High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans.

Genome medicine, 12(1):59 pii:10.1186/s13073-020-00758-x.

BACKGROUND: Dietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consistency and temporal responses of the gut microbiome to glycans is critical for rationally developing and deploying these compounds as therapeutics.

METHODS: We investigated the effect of two chemically distinct glycans (fructooligosaccharides and polydextrose) through three clinical studies conducted with 80 healthy volunteers. Stool samples, collected at dense temporal resolution (~ 4 times per week over 10 weeks) and analyzed using shotgun metagenomic sequencing, enabled detailed characterization of participants' microbiomes. For analyzing the microbiome time-series data, we developed MC-TIMME2 (Microbial Counts Trajectories Infinite Mixture Model Engine 2.0), a purpose-built computational tool based on nonparametric Bayesian methods that infer temporal patterns induced by perturbations and groups of microbes sharing these patterns.

RESULTS: Overall microbiome structure as well as individual taxa showed rapid, consistent, and durable alterations across participants, regardless of compound dose or the order in which glycans were consumed. Significant changes also occurred in the abundances of microbial carbohydrate utilization genes in response to polydextrose, but not in response to fructooligosaccharides. Using MC-TIMME2, we produced detailed, high-resolution temporal maps of the microbiota in response to glycans within and across microbiomes.

CONCLUSIONS: Our findings indicate that dietary glycans cause reproducible, dynamic, and differential alterations to the community structure of the human microbiome.

RevDate: 2020-07-03

Reitmeier S, Kiessling S, Clavel T, et al (2020)

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes.

Cell host & microbe pii:S1931-3128(20)30343-7 [Epub ahead of print].

Lifestyle, obesity, and the gut microbiome are important risk factors for metabolic disorders. We demonstrate in 1,976 subjects of a German population cohort (KORA) that specific microbiota members show 24-h oscillations in their relative abundance and identified 13 taxa with disrupted rhythmicity in type 2 diabetes (T2D). Cross-validated prediction models based on this signature similarly classified T2D. In an independent cohort (FoCus), disruption of microbial oscillation and the model for T2D classification was confirmed in 1,363 subjects. This arrhythmic risk signature was able to predict T2D in 699 KORA subjects 5 years after initial sampling, being most effective in combination with BMI. Shotgun metagenomic analysis functionally linked 26 metabolic pathways to the diurnal oscillation of gut bacteria. Thus, a cohort-specific risk pattern of arrhythmic taxa enables classification and prediction of T2D, suggesting a functional link between circadian rhythms and the microbiome in metabolic diseases.

RevDate: 2020-07-03

Cordeiro RA, de Andrade ARC, Portela FVM, et al (2020)

Proposal for a microcosm biofilm model for the study of vulvovaginal candidiasis.

Biofouling [Epub ahead of print].

This study proposes a microcosm biofilm (MiB) model for the study of vulvovaginal candidiasis (VVC). Different conditions that mimic the vaginal environment were tested for MiB formation. The best growth conditions were obtained with samples incubated in vaginal fluid simulator medium pH 4.5 at 35 °C under a microaerophilic atmosphere. MiBs were evaluated for growth kinetics, fluconazole susceptibility and morphology. Samples containing high numbers of bacteria were analyzed for metagenomics. At 48 h, MiBs presented a higher cell density (CFU ml-1), a higher biomass and tolerance to fluconazole than their corresponding monospecies biofilms. Morphological analysis of MiBs revealed blastoconidia preferentially adhered to epithelial cells. Abundant Lactobacillus spp. were detected in two clinical samples; their MiBs showed a lower biomass and a higher fluconazole susceptibility. The proposed model proved to be a useful tool for the study of the complex microbial relationship in the vaginal environment, and may help to find new strategies for VVC control.

RevDate: 2020-07-03

Peláez A, McLeish MJ, Paswan RR, et al (2020)

Ecological fitting is the forerunner to diversification in a plant virus with broad host range.

Journal of evolutionary biology [Epub ahead of print].

The evolution and diversification of ssRNA plant viruses are often examined under reductionist conditions that ignore potentially much wider biotic interactions. The host range of a plant virus is central to interactions at higher levels that are organised by both fitness and ecological criteria. Here we employ a strategy to minimise sampling biases across distinct plant communities, and combine it with a high throughput sequencing approach to examine the influence of four habitats on the evolution of Watermelon mosaic virus (WMV). Local, regional, and global levels of genetic diversity that correspond to spatial and temporal extents, are used to infer haplotype relationships using network and phylogenetic approaches. We find that the incidence and genetic diversity of WMV were structured significantly by host species and habitat type. A single haplotype that infected 11 host species of a total of 24, showed that few constraints on host species use exist in the crop communities. When the evolution of WMV was examined at broader levels of organisation, we found variation in genetic diversity and contrasting host use footprints that broadly corresponded to habitat effects. The findings demonstrated that non-deterministic ecological factors structured the genetic diversity of WMV. Habitat-driven constraints underlie host use preferences.

RevDate: 2020-07-03

Guk J, Guedj J, Burdet C, et al (2020)

Modeling the effect of DAV132, a novel colon-targeted adsorbent, on fecal concentrations of moxifloxacin and gut microbiota diversity in healthy volunteers.

Clinical pharmacology and therapeutics [Epub ahead of print].

To prevent antibiotic-induced perturbations on gut microbiota, DAV132, a novel colon-targeted adsorbent, which sequesters antibiotic residues in the lower gastrointestinal tract was developed. We built an integrated pharmacological model of how DAV132 reduces fecal free moxifloxacin (MXF) and preserves gut microbiota. We used plasma and fecal free MXF concentrations, and Shannon diversity index from 16S rRNA gene metagenomics analysis of fecal microbiota, of 143 healthy volunteers assigned randomly to receive MXF only, or with ten DAV132 dose regimens, or to a control group. We modeled reduced fecal MXF concentrations using a transit model for DAV132 kinetics and a Michaelis-Menten model with an effect of the amount of activated charcoal on adsorption efficacy. Changes in MXF-induced perturbations on gut microbiota diversity were then quantified through a turn-over model with the Emax model. With the developed model, the efficiency of pharmacokinetic antagonism and its consequences on gut microbiota diversity were quantified.

RevDate: 2020-07-03

Huang G, Wang X, Hu Y, et al (2020)

Diet drives convergent evolution of gut microbiomes in bamboo-eating species.

Science China. Life sciences pii:10.1007/s11427-020-1750-7 [Epub ahead of print].

Gut microbiota plays a critical role in host physiology and health. The coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological niche. Multiple factors such as host diet and phylogeny modulate the structure and function of gut microbiota. However, the relative contribution of each factor in shaping the structure of gut microbiota remains unclear. The giant (Ailuropoda melanoleuca) and red (Ailurus styani) pandas belong to different families of order Carnivora. They have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent evolution. Here, we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome sequencing. We found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous relatives. This indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within Arctoidea. Metagenomic analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 biosynthesis. These findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species.

RevDate: 2020-07-03

Jang SW, Yoou MH, Hong WJ, et al (2020)

Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition.

Rice (New York, N.Y.), 13(1):44 pii:10.1186/s12284-020-00403-6.

Rice (Oryza sativa. L) has been intensively studied to ensure a stable global supply of this commodity in the face of rapid global climate change. A critical factor that decreases crop yield is drought, which has been analyzed in various ways through many researches. Microbiome-based studies of rice investigate the symbiosis between rice and bacteria, which has been proposed as a way to overcome problems caused by drought. Several rice-associated metagenomic profiles obtained under drought conditions have been reported since the advent of next generation sequencing (NGS) technology. To elucidate the future diversity of plants and microorganisms and to promote sustainable agriculture, we reanalyzed 64 of the publicly available 16S amplicon sequencing data produced under drought condition. In the process of integrating data sets, however, we found an inconsistency that serves as a bottleneck for microbiome-based sustainability research. While this report provides clues about the composition of the microbiome under the drought conditions, the results are affected by differences in the location of the experiments, sampling conditions, and analysis protocols. Re-analysis of amplicon sequencing data of the soil microbiome in rice fields suggests that microbial composition shifts in response to drought condition and the presence of plants. Among the bacteria involved, the phylum Proteobacteria appears to play the most important role in the survival of rice under drought condition.

RevDate: 2020-07-03

Pinto OHB, Costa FS, Rodrigues GR, et al (2020)

Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids.

Microbial ecology pii:10.1007/s00248-020-01548-z [Epub ahead of print].

Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.

RevDate: 2020-07-03

Seppey M, Manni M, EM Zdobnov (2020)

LEMMI: A continuous benchmarking platform for metagenomics classifiers.

Genome research pii:gr.260398.119 [Epub ahead of print].

Studies of microbiomes are booming, along with the diversity of computational approaches to make sense out of the sequencing data and the volumes of accumulated microbial genotypes. A swift evaluation of newly published methods and their improvements against established tools is necessary to reduce the time between the method's release and its adoption in microbiome analyses. The LEMMI platform offers a novel approach for benchmarking software dedicated to metagenome composition assessments based on read classification. It enables the integration of newly published methods in an independent and centralized benchmark designed to be continuously open to new submissions. This allows developers to be proactive regarding comparative evaluations and guarantees that any promising methods can be assessed side-by-side with established tools quickly after their release. Moreover, LEMMI enforces an effective distribution through software containers to ensure long term availability of all methods. Here, we detail the LEMMI workflow and discuss the performances of some previously unevaluated tools. We see this platform eventually as a community-driven effort where method developers can showcase novel approaches and get unbiased benchmarks for publications, while users can make informed choices and obtain standardized and easy-to-use tools.

RevDate: 2020-07-03

Li M, Yang F, Lu Y, et al (2020)

Identification of Enterococcus faecalis in a patient with urinary-tract infection based on metagenomic next-generation sequencing: a case report.

BMC infectious diseases, 20(1):467 pii:10.1186/s12879-020-05179-0.

BACKGROUND: Urinary tract infection (UTI) caused by various pathogenic microorganisms is ubiquitous in the parts of the urinary system such as kidney, ureter, bladder, and urethra. Currently, clinical detection of UTI is mainly focused on urine culture; however, the diagnostic value of urine culture remains limited due to the time-consuming procedure and low detection rate, especially in patients who have used antibiotics. Generally, treatment for UTI relies on empirical medication rather than pathogen diagnosis, which leads to the inappropriate use of antimicrobial agents and a significant increase in resistant strains. Comparatively, metagenomic next-generation sequencing (mNGS) is capable of overcoming the disadvantages of clinical culture, and identifying pathogens for further treatment.

CASE PRESENTATION: A 33-year-old male patient was admitted to hospital with a high fever and chills. None of his autoimmune disease or thyroid function related indicators were positive, and he had no risk of endocarditis. His white blood cell count, C-reactive protein, procalcitonin, interleukin 6, and neutrophil proportion were markedly elevated. He was initially diagnosed as having an infection of unknown etiology. Since empirical treatment of Sulperazon and Metronidazole did not relieve his symptoms, both the blood and urine specimens were examined using traditional culture, serological testing, and mNGS assay. Traditional culture and serological testing produced negative results, while the mNGS assay revealed the presence of a potential pathogen, Enterococcus faecalis, in the urine specimen, which was further confirmed by both Sanger sequencing and qPCR analysis. A CT scan of the patient's whole abdomen showed stones in the right kidney. Once targeted antibiotic therapy was administered, the patient recovered quickly.

CONCLUSIONS: Our case illustrated that mNGS, as a novel culture-independent approach, demonstrated the capability of rapid, sensitive, and accurate pathogen identification. Furthermore, this technology provides strong support for guiding clinicians to determine appropriate treatment.

RevDate: 2020-07-02

Ma C, Lo PK, Xu J, et al (2020)

Molecular mechanisms underlying lignocellulose degradation and antibiotic resistance genes removal revealed via metagenomics analysis during different agricultural wastes composting.

Bioresource technology, 314:123731 pii:S0960-8524(20)31003-8 [Epub ahead of print].

In this study, the differences on the physico-chemical parameters, lignocellulose degradation, dynamic succession of microbial community, gene expression of carbohydrate-active enzymes and antibiotics resistance genes were compared during composting systems of bagasse pith/pig manure (BP) and manioc waste/pig manure (MW). The results revealed that biodegradation rates of organic matter, cellulose, hemicellulose and lignin (29.14%, 17.53%,45.36% and 36.48%) in BP were higher than those (15.59%, 16.74%, 41.23% and 29.77%) in MW. In addition, the relative abundance of Bacillus, Luteimonas, Clostridium, Pseudomonas, Streptomyces and expression of genes encoding carbohydrate- active enzymes in BP were higher than those in MW based on metagenomics sequencing. During composting, antibiotics and antibiotic resistance genes were substantially reduced, but the removal efficiency was divergent in the both samples. Taken together, metagenomics analysis was a potential method for evaluating lignocellulose's biodegradation process and determining the elimination of antibiotic and antibiotic resistance genes from different composting sources of biomass.

RevDate: 2020-07-02

Yang L, Hou K, Zhang B, et al (2020)

Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut.

The Science of the total environment, 741:140423 pii:S0048-9697(20)33945-0 [Epub ahead of print].

With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of -80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and -80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.

RevDate: 2020-07-02

Sheludko YV, WD Fessner (2020)

Winning the numbers game in enzyme evolution - fast screening methods for improved biotechnology proteins.

Current opinion in structural biology, 63:123-133 pii:S0959-440X(20)30075-0 [Epub ahead of print].

The booming demand for environmentally benign industrial processes relies on the ability to quickly find or engineer a biocatalyst suitable to ideal process conditions. Both metagenomic approaches and directed evolution involve the screening of huge libraries of protein variants, which can only be managed reasonably by flexible platforms for (ultra)high-throughput profiling against the desired criteria. Here, we review the most recent additions toward a growing toolbox of versatile assays using fluorescence, absorbance and mass spectrometry readouts. While conventional solution based high-throughput screening in microtiter plate formats is still important, the implementation of novel screening protocols for microfluidic cell or droplet sorting systems supports technological advances for ultra-high-frequency screening that now can dramatically reduce the timescale of engineering projects. We discuss practical issues of scope, scalability, sensitivity and stereoselectivity for the improvement of biotechnologically relevant enzymes from different classes.

RevDate: 2020-07-02

Yang Y, Wu R, Hu J, et al (2020)

Dominant denitrifying bacteria are important hosts of antibiotic resistance genes in pig farm anoxic-oxic wastewater treatment processes.

Environment international, 143:105897 pii:S0160-4120(20)31852-3 [Epub ahead of print].

The anoxic-oxic (A/O) wastewater treatment process that is widely used in pig farms in China is an important repository for antibiotic resistance genes (ARGs). However, the distribution of ARGs and their hosts in the A/O process has not been well characterized. In this study, the wastewaters in the anoxic and oxic tanks for A/O processes were collected from 38 pig farms. The concentrations of 20 subtypes of ARGs, 5 denitrification-related genes, 2 integrons, and bacterial community composition were investigated. Bacterial genome binning was performed using metagenome sequencing. In this study, 20 subtypes of ARGs and integrons were detected in all sampling sites. A total of 16 of the 20 subtypes of ARGs were detected with the highest abundance in anoxic tanks, and sul1 was detected with a maximum average abundance of 19.21 ± 0.24 log10 (copies/mL). Cooccurrence patterns were observed for some genes in the pig farm A/O process, such as sul1 and intl1, sul1 and tetG, and tetO and tetW. There was a significant cooccurrence pattern between the dominant denitrifying bacteria and some ARGs (blaTEM, ermB, tetC, tetH and tetQ), so the dominant denitrifying bacteria were considered to be potential ARG hosts. In addition, 170 highly abundant bacterial genome bins were assembled and further confirmed that the denitrifying bacteria Brachymonas, Candidatus Competibacter, Thiobacillus and Steroidobacter were the important ARG hosts in the pig farm A/O process, providing a useful reference for the surveillance and risk management of ARGs in pig farm wastewater.

RevDate: 2020-07-02

Guilloux CA, Lamoureux C, Beauruelle C, et al (2020)

Porphyromonas: A neglected potential key genus in human microbiomes.

Anaerobe pii:S1075-9964(20)30086-X [Epub ahead of print].

Anaerobes form a large part of microbial communities, and have begun to be specifically studied in both healthy and pathologic contexts. Porphyromonas is one of the top ten anaerobic taxa in the microbiome (anaerobiome) in healthy subjects. However, to date, most studies focused on the deleterious role of P. gingivalis, the most widely described species. Interestingly, targeted metagenomics reveals Porphyromonas other than gingivalis (POTG), highlighting other species such as P. catoniae or P. pasteri as potential biomarkers in disease progression or pathogen colonization susceptibility. From the sparse data, it appears that the Porphyromonas genus may also be a relevant target of investigation in several pulmonary diseases. Moreover, deciphering cutaneous, gastric and oral microbiomes hint that Porphyromonas may be a genus of interest in non-pulmonary diseases. This review aims to summarize the major data on POTG and to report their impact on the various human microbiomes in different clinical states.

RevDate: 2020-07-02

Williams SC, Frew JW, JG Krueger (2020)

A Systematic Review andCritical Appraisal of Metagenomic and Culture Studies in Hidradenitis Suppurativa.

Experimental dermatology [Epub ahead of print].

BACKGROUND: Hidradenitis Suppurativa (HS), also known as acne inversa, is a chronic inflammatory skin disease with still largely unknown pathogenesis. While infectious organisms have been identified in lesions of the disease since the 1980s, questions remain over the role that bacteria and microbiome play. Recent studies using 16S ribosomal RNA genesequencing and larger culture-based studies have begun to paint a clearer picture of the microbial world of HS. With this systematic review we summarizeall the work that has been done to date in HS bacteriology, analyze potential pitfalls and limitations of the current studies, and address future directions of investigation.

METHODS: This systematic review attempted to collate and analyze all bacteriology studies done to date. This review was prospectively registered with PROSPERO (1670769) performed in line with the PRISMA checklist.

RESULTS: 22 studies were identified comprising 862 individual HS patients for culture studies and 206 HS patients for 16S rRNA genesequencing studies. Methodology tended to be varied, with different sampling, culturing and sequencing methods as well as amount of analysis and stratification of patients.

CONCLUSIONS: Bacteria identified as elevated in HS lesions in sequencing studies as well as grown from HS lesions in culture studies are identified and discussed. These primarily included the anerobic Gram-negative bacilli Prevotella, Porphyromonas, and Fusibacterium, the Gram-positive bacilli Corynebacterium, and the Gram-positive cocci Staphylococcus, Streptococcus and Parvimonas. Potential interactions, as well as work in other disease models with related bacteria are also discussed. Areas of further investigation include in vitro studies of interactions between bacteria and keratinocytes, gut and oral microbiome studies and deep sequencing studies for virulence and phage factors.

RevDate: 2020-07-02

Hameed M, Khan S, Xu J, et al (2020)

Detection of Japanese Encephalitis Virus in Mosquitoes from Xinjiang during Next Generation Sequencing Arboviral Surveillance.

Transboundary and emerging diseases [Epub ahead of print].

A total of 548 mosquitoes were collected from different animal farms located near to highly populated cities in Xinjiang, and were subjected to metagenomic Next Generation Sequencing (mNGS). The mNGS data demonstrated that 18842 (XJ1 strain) and 1077 (XJ2 strain) of Japanese encephalitis virus (JEV) related reads were detected in XJ1 and XJ2 mosquito samples collected from Wushi and Wensu counties of Aksu area, which accounted for 0.032% and 0.006% of the total clean reads generated from XJ1 and XJ2 samples, respectively. The Bayesian molecular phylogenetic analysis suggested that XJ1 and XJ2 strains belonged to JEV genotype III, and were clustered with JEV strains isolated in China. Notably, Bayesian molecular time line phylogeny revealed that XJ1 strain shared its MRCA with JEV GSS strain about 67 YA, suggesting that XJ1 strain likely originated from linages closely related to GSS strain and spread to Xinjiang later. Overall, these findings suggest that Xinjiang was probably not free from JEV, and thus a further surveillance of JEV is required in Xinjiang.

RevDate: 2020-07-02

Szeinbaum N, Nunn BL, Cavazos AR, et al (2020)

Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction.

Environmental microbiology reports [Epub ahead of print].

Soluble ligand-bound Mn(III) can support anaerobic microbial respiration in diverse aquatic environments. Thus far, Mn(III) reduction has only been associated with certain Gammaproteobacteria. Here, we characterized microbial communities enriched from Mn-replete sediments of Lake Matano, Indonesia. Our results provide the first evidence for biological reduction of soluble Mn(III) outside the Gammaproteobacteria. Metagenome assembly and binning revealed a novel betaproteobacterium, which we designate "Candidatus Dechloromonas occultata." This organism dominated the enrichment and expressed a porin-cytochrome c complex typically associated with iron-oxidizing Betaproteobacteria and a novel cytochrome c-rich protein cluster (Occ), including an undecaheme putatively involved in extracellular electron transfer. This occ gene cluster was also detected in diverse aquatic bacteria, including uncultivated Betaproteobacteria from the deep subsurface. These observations provide new insight into the taxonomic and functional diversity of microbially-driven Mn(III) reduction in natural environments. This article is protected by copyright. All rights reserved.

RevDate: 2020-07-02

Jayasinghe TN, Vatanen T, Chiavaroli V, et al (2020)

Differences in Compositions of Gut Bacterial Populations and Bacteriophages in 5-11 Year-Olds Born Preterm Compared to Full Term.

Frontiers in cellular and infection microbiology, 10:276.

Preterm infants are exposed to major perinatal, post-natal, and early infancy events that could impact on the gut microbiome. These events include infection, steroid and antibiotic exposure, parenteral nutrition, necrotizing enterocolitis, and stress. Studies have shown that there are differences in the gut microbiome during the early months of life in preterm infants. We hypothesized that differences in the gut microbial composition and metabolites in children born very preterm persist into mid-childhood. Participants were healthy prepubertal children aged 5-11 years who were born very preterm (≤32 weeks of gestation; n = 51) or at term (37-41 weeks; n = 50). We recorded the gestational age, birth weight, mode of feeding, mode of birth, age, sex, and the current height and weight of our cohort. We performed a multi'omics [i.e., 16S rRNA amplicon and shotgun metagenomic sequencing, SPME-GCMS (solid-phase microextraction followed by gas chromatography-mass spectrometry)] analysis to investigate the structure and function of the fecal microbiome (as a proxy of the gut microbiota) in our cross-sectional cohort. Children born very preterm were younger (7.8 vs. 8.3 years; p = 0.034), shorter [height-standard deviation score (SDS) 0.31 vs. 0.92; p = 0.0006) and leaner [BMI (body mass index) SDS -0.20 vs. 0.29; p < 0.0001] than the term group. Children born very preterm had higher fecal calprotectin levels, decreased fecal phage richness, lower plasma arginine, lower fecal branched-chain amino acids and higher fecal volatile (i.e., 3-methyl-butanoic acid, butyrolactone, butanoic acid and pentanoic acid) profiles. The bacterial microbiomes did not differ between preterm and term groups. We speculate that the observed very preterm-specific changes were established in early infancy and may impact on the capacity of the very preterm children to respond to environmental changes.

RevDate: 2020-07-02

Kumar V, R Chandra (2020)

Metagenomics analysis of rhizospheric bacterial communities of Saccharum arundinaceum growing on organometallic sludge of sugarcane molasses-based distillery.

3 Biotech, 10(7):316.

The present paper aims to explore the rhizospheric bacterial communities associated with Saccharum arundinaceum grown on organometallic pollutants-rich hazardous distillery sludge. The sequence analysis of 16S rRNA V3-V4 hypervariable region with Illumina MiSeq platform showed 621,897 OTUs derived from rhizospheric and non-rhizospheric distillery sludge samples out of 1,191,014 and 901,757 sequences read, respectively. The major phyla detected in rhizospheric sludge sample were Proteobacteria (50%), Bacteriodetes (33%), Firmicutes (5%) Gemmatimonadetes (2%), Chloroflexi (2%), and Tenericutes (2%). The dominant three genera were detected as Rheinheimera (21%), Sphingobacterium (17%), and Idiomarina (8%). In addition, other minor genera such as uncultured Bacillus (4%), Acidothermus (4%), Bacillus (3%), Pseudomonas (2%), Flavobacterium (2%), uncultured bacterium (2%), Parapedobacter (2%), Alcanivorax (2%), Acholeplasma (2%), Hyphomonas (1%), and Aquamicrobium were also detected (1%) in rhizospheric sludge. Our results suggested that rhizospheric bacterial communities associated with S. arundinaceum were substantially different in richness, diversity, and relative abundance of taxa compared to non-rhizospheric sludge. Further, the comparative organic pollutant analysis from non-rhizospheric and rhizospheric sludge samples through GC-MS analysis revealed the disappearance of few compounds and generation of some compounds as new metabolic products by the activity of rhizospheric bacterial communities. The results of this study will be helpful in understanding the role of rhizospheric bacterial communities responsible for degradation and detoxification of complex organometallic waste and, thus, can help in designing appropriate phytoremediation studies for eco-restoration of polluted sites.

RevDate: 2020-07-02

Dong J, Liu S, Zhang Y, et al (2020)

A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas.

Frontiers in microbiology, 11:1061.

The comparison of metagenomes is crucial for studying the relationship between microbial communities and environmental factors. One recently published alignment-free whole metagenome comparison method based on k-mer frequencies, Libra, showed higher resolutions than the present fastest method, Mash, on whole metagenomic sequencing reads, but it did not perform as well on the assembled contigs. Here, we developed a new alignment-free tool, KmerFreqCalc, for the comparison of the whole metagenomic data, which first calculated the frequencies of both forward and reverse complementary sequences of k-mers like Mash and then computed the cosine distance between the samples based on k-mer frequency vectors like Libra. We applied KmerFreqCalc on the assembled contigs of the gut microbiomes of wild giant pandas and compared the results to Libra and Mash. The results indicated that KmerFreqCalc was able to detect the subtle difference between giant panda samples caused by seasonal diet change, showing better clustering than Libra and Mash. Therefore, KmerFreqCalc has high resolution and accuracy for assembled contigs, being very suitable for comparison of samples with low dissimilarity.

RevDate: 2020-07-02

Hofmeyr S, Egan R, Georganas E, et al (2020)

Terabase-scale metagenome coassembly with MetaHipMer.

Scientific reports, 10(1):10689 pii:10.1038/s41598-020-67416-5.

Metagenome sequence datasets can contain terabytes of reads, too many to be coassembled together on a single shared-memory computer; consequently, they have only been assembled sample by sample (multiassembly) and combining the results is challenging. We can now perform coassembly of the largest datasets using MetaHipMer, a metagenome assembler designed to run on supercomputers and large clusters of compute nodes. We have reported on the implementation of MetaHipMer previously; in this paper we focus on analyzing the impact of very large coassembly. In particular, we show that coassembly recovers a larger genome fraction than multiassembly and enables the discovery of more complete genomes, with lower error rates, whereas multiassembly recovers more dominant strain variation. Being able to coassemble a large dataset does not preclude one from multiassembly; rather, having a fast, scalable metagenome assembler enables a user to more easily perform coassembly and multiassembly, and assemble both abundant, high strain variation genomes, and low-abundance, rare genomes. We present several assemblies of terabyte datasets that could never be coassembled before, demonstrating MetaHipMer's scaling power. MetaHipMer is available for public use under an open source license and all datasets used in the paper are available for public download.

RevDate: 2020-07-02

Parbie PK, Mizutani T, Ishizaka A, et al (2020)

Fecal microbiome composition in healthy adults in Ghana.

Japanese journal of infectious diseases [Epub ahead of print].

Current studies have indicated association of gut microbiome composition with varieties of disorders including infectious diseases. The microbiome composition is different among races and countries, possibly resulting in diversified interaction between host immune and gut microbiome. Characterization of the baseline microbiota in healthy people is an essential step to understand this biological interaction in individual populations. However, data on gut/fecal microbiome has not been accumulated in West Africa. In the present study, we examined fecal microbiome composition in healthy adults in Ghana. The 16S rRNA gene libraries were prepared using bacteria fractions derived from 55 Ghanaian adults and subjected to next generation sequencing. Fecal microbiome of Ghanaian adults was dominated by Firmicutes (Faecalibacterium, Subdoligranulum, and Ruminococcaceae UCG-014), Proteobacteria (Escherichia-Shigella and Klebsiella), and Bacteroidetes (Prevotella 9 and Bacteroides), consistent with previous observations in African cohorts. Analysis found difference in composition and lower diversity of fecal microbiome in our cohort compared to non-African countries. This is the first study that describes substantial fecal microbiome data obtained by using high throughput metagenomic tools in Ghana. These data would be valuable as a basis for determination of the association between fecal microbiome and progression of varieties of diseases in West African populations.

RevDate: 2020-07-02

Zhang D, You F, He Y, et al (2020)

Isolation and characterization of the first freshwater cyanophage infecting Pseudanabaena.

Journal of virology pii:JVI.00682-20 [Epub ahead of print].

Cyanobacteria are the major primary producers in both freshwater and marine environments. However, the majority of freshwater cyanophages remain unknown due to the limited number of cyanophage isolates. In this study, we present a novel lytic freshwater cyanophage PA-SR01 which was isolated from Singapore Serangoon Reservoir. To our knowledge, this is the first isolate of cyanophage that has been found to infect the cyanobacterium Pseudanabaena PA-SR01 has a narrow host range, a short latent period and is chloroform sensitive. Distinct from the majority of cyanophage isolates, PA-SR01 has a tail-less morphology. It is a double-stranded DNA virus with a 137,012 bp genome. Functional annotation for the predicted open reading frames (ORFs) of PA-SR01 genome identified genes with putative function related to DNA metabolism, structural protein, lysis, host-derived metabolic genes and DNA packaging. Out of 166 predicted ORFs, only 17 ORFs have homology with genes with known function. Phylogenetic analysis of the major capsid protein and terminase large subunit further suggests that Phage PA-SR01 is evolutionary distinct from known cyanophages. Metagenomics sequence recruitment onto PA-SR01 genome indicates that PA-SR01 represents a new evolutionary lineage of phage which shares considerable genetic similarities with phage sequences in aquatic environments and could play key ecological roles.IMPORTANCE This study presents the isolation of the very first freshwater cyanophage PA-SR01 infecting Pseudanabaena and fills important knowledge gap on freshwater cyanophage as well as cyanophages infecting Pseudanabaena.

RevDate: 2020-07-02

Shimizu K, Takahashi A, Motooka D, et al (2020)

Fecal Gram staining of phagocytosed bacteria to differentiate methicillin-resistant Staphylococcus aureus: A case report.

Antibiotic-associated diarrhea is a relatively common problem, and the main bacterial cause is Clostridioides difficile followed by Staphylococcus aureus and other pathogens. The diagnostic procedure for methicillin-resistant S. aureus enteritis is not well established. Phagocytosis is a key antimicrobial process involved in host defense. Phagocytosed bacteria identified by Gram staining are one marker to identify causative microorganisms and select subsequent treatment strategies. However, there are few reports on fecal Gram staining using phagocytosed bacteria as a target for diarrhea treatment. We report the successful use of fecal Gram staining to diagnose and treat methicillin-resistant S. aureus enteritis.

RevDate: 2020-07-02
CmpDate: 2020-07-02

Rho M, WJ Song (2020)

Discovery of Novel Gene Functions by Chemistry-Guided Targeted Sequence Analysis.

Biochemistry, 59(1):10-11.

RevDate: 2020-07-02
CmpDate: 2020-07-02

Roossinck MJ (2019)

Viruses in the phytobiome.

Current opinion in virology, 37:72-76.

The phytobiome, defined as plants and all the entities that interact with them, is rich in viruses, but with the exception of plant viruses of crop plants, most of the phytobiome viruses remain very understudied. This review focuses on the neglected portions of the phytobiome, including viruses of other microbes interacting with plants, viruses in the soil, viruses of wild plants, and relationships between viruses and the vectors of plant viruses.

RevDate: 2020-07-01

Levade I, Saber MM, Midani F, et al (2020)

Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study.

The Journal of infectious diseases pii:5866141 [Epub ahead of print].

BACKGROUND: Susceptibility to Vibrio cholerae infection is impacted by blood group, age, and pre-existing immunity, but these factors only partially explain who becomes infected. A recent study used 16S rRNA amplicon sequencing to quantify the composition of the gut microbiome and identify predictive biomarkers of infection with limited taxonomic resolution.

METHODS: To achieve increased resolution of gut microbial factors associated with V. cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera.

RESULTS: Using machine learning, we resolved species, strains, gene families, and cellular pathways in the microbiome at the time of exposure to V. cholerae to identify markers that predict infection and symptoms. Use of metagenomic features improved the precision and accuracy of prediction relative to 16S sequencing. We also predicted disease severity, although with greater uncertainty than our infection prediction. Species within the genera Prevotella and Bifidobacterium predicted protection from infection, and genes involved in iron metabolism also correlated with protection.

CONCLUSION: Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera.

RevDate: 2020-07-01

Oh TG, Kim SM, Caussy C, et al (2020)

A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis.

Cell metabolism pii:S1550-4131(20)30306-5 [Epub ahead of print].

Dysregulation of the gut microbiome has been implicated in the progression of non-alcoholic fatty liver disease (NAFLD) to advanced fibrosis and cirrhosis. To determine the diagnostic capacity of this association, we compared stool microbiomes across 163 well-characterized participants encompassing non-NAFLD controls, NAFLD-cirrhosis patients, and their first-degree relatives. Interrogation of shotgun metagenomic and untargeted metabolomic profiles by using the random forest machine learning algorithm and differential abundance analysis identified discrete metagenomic and metabolomic signatures that were similarly effective in detecting cirrhosis (diagnostic accuracy 0.91, area under curve [AUC]). Combining the metagenomic signature with age and serum albumin levels accurately distinguished cirrhosis in etiologically and genetically distinct cohorts from geographically separated regions. Additional inclusion of serum aspartate aminotransferase levels, which are increased in cirrhosis patients, enabled discrimination of cirrhosis from earlier stages of fibrosis. These findings demonstrate that a core set of gut microbiome species might offer universal utility as a non-invasive diagnostic test for cirrhosis.

RevDate: 2020-07-01

Horodesky A, Castilho-Westphal GG, Pont GD, et al (2020)

Metagenomic analysis of the bacterial microbiota associated with cultured oysters (Crassostrea sp.) in estuarine environments.

Anais da Academia Brasileira de Ciencias, 92(suppl 1):e20180432 pii:S0001-37652020000201019.

In this work, we identified the bacterial microbiota associated with farmed oystersin estuarine regions of four states in the north eastern region of Brazil. During the drought and rainy seasons, for eight months, twenty oysters were sampled seasonally from seven different marine farms. In the laboratory, DNA extraction, amplification, and sequencing of the 16S rRNA gene were performed to establish the taxonomic units. We identified 106 genera of bacteria belonging to 103 families, 70 orders, 39 classes, and 21 phyla. Out of the total, 40 of the genera represented bacteria potentially pathogenic to humans; of these, nine are known to cause foodborne diseases and six are potentially pathogenic to oysters. The most prevalent genera were Mycoplasma, Propionigenium, Psychrilyobacter, and Arcobacter. The results indicate the need for more systematic monitoring of bacteria of the genus Mycoplasma in oyster farming operations in the Brazilian north eastern region. Currently, Mycoplasma is not one of the microorganisms analysed and monitored by order of Brazilian legislation during the oyster production and/or commercialization process, even though this genus was the most prevalent at all sampling points and presents pathogenic potential both for oysters and for consumers.

RevDate: 2020-07-01

Chu C, Wu ZY, Huang QR, et al (2020)

[Effect of Organic Matter Promotion on Nitrogen-Cycling Genes and Functional Microorganisms in Acidic Red Soils].

Huan jing ke xue= Huanjing kexue, 41(5):2468-2475.

The application of exogenous organic matter is considered the main method of increasing the organic matter content of acidic red soils. Nitrogen is an important limiting factor for soil fertility. Changes to the soil ecosystem under organic matter promotion can affect soil nitrogen cycling and related functional microorganisms; however, there have been no studies on this aspect. Acidic upland red soils, with or without long-term organic fertilizer application, were chosen as the research materials in this study. Based on metagenomic sequencing and alignment in the nitrogen-cycling gene database, the present study aimed to investigate the effect of organic matter promotion on nitrogen-cycling genes and functional microorganisms in acidic red soils, which had been amended with exogenous organic matter for 32 years. The results showed that organic matter promotion in acidic soils increased the total organic carbon and total nitrogen content, and alleviated soil acidification. Organic matter promotion increased the soil net nitrification activity and potential for ammoxidation. Organic matter promotion increased the abundance of amoA genes (encoding ammonia monooxygenase) and nar, nap, nir, nor, and nos genes (encoding denitrification reductase); decreased the abundance of hao genes (encoding hydroxylamine oxidase) and nrf genes related to the dissimilatory nitrate reduction to ammonia; increased the abundance of glnA, gdh, glsA, ansB, and nao genes related to organic nitrogen metabolism; altered the abundance of functional genes related to assimilatory nitrate reduction; and changed the community composition of nitrogen-cycling microorganisms. After organic matter promotion, alleviation of soil acidification and enhancement of total organic carbon were the most important factors that affected the abundance of nitrogen-cycling genes and the community composition of functional microorganisms. Our results comprehensively investigated the inorganic and organic nitrogen-cycling genes, and correlated the functional genes, microbial populations, and functional activities in the ammonia oxidizing process, which provided supporting data to understand the nitrogen-cycling characteristics of acidic red soils and provided ideas for acidic soil improvement.

RevDate: 2020-07-01

Stultiens K, van Kessel MAHJ, Frank J, et al (2020)

Diversity, enrichment, and genomic potential of anaerobic methane- and ammonium-oxidizing microorganisms from a brewery wastewater treatment plant.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10748-z [Epub ahead of print].

Anaerobic wastewater treatment offers several advantages; however, the effluent of anaerobic digesters still contains high levels of ammonium and dissolved methane that need to be removed before these effluents can be discharged to surface waters. The simultaneous anaerobic removal of methane and ammonium by denitrifying (N-damo) methanotrophs in combination with anaerobic ammonium-oxidizing (anammox) bacteria could be a potential solution to this challenge. After a molecular survey of a wastewater plant treating brewery effluent, indicating the presence of both N-damo and anammox bacteria, we started an anaerobic bioreactor with a continuous supply of methane, ammonium, and nitrite to enrich these anaerobic microorganisms. After 14 months of operation, a stable enrichment culture containing two types of 'Candidatus Methylomirabilis oxyfera' bacteria and two strains of 'Ca. Brocadia'-like anammox bacteria was achieved. In this community, anammox bacteria converted 80% of the nitrite with ammonium, while 'Ca. Methylomirabilis' contributed to 20% of the nitrite consumption. The analysis of metagenomic 16S rRNA reads and fluorescence in situ hybridization (FISH) correlated well and showed that, after 14 months, 'Ca. Methylomirabilis' and anammox bacteria constituted approximately 30 and 20% of the total microbial community. In addition, a substantial part (10%) of the community consisted of Phycisphaera-related planctomycetes. Assembly and binning of the metagenomic sequences resulted in high-quality draft genome of two 'Ca. Methylomirabilis' species containing the marker genes pmoCAB, xoxF, and nirS and putative NO dismutase genes. The anammox draft genomes most closely related to 'Ca. Brocadia fulgida' included the marker genes hzsABC, hao, and hdh. Whole-reactor and batch anaerobic activity measurements with methane, ammonium, nitrite, and nitrate revealed an average anaerobic methane oxidation rate of 0.12 mmol h-1 L-1 and ammonium oxidation rate of 0.5 mmol h-1 L-1. Together, this study describes the enrichment and draft genomes of anaerobic methanotrophs from a brewery wastewater treatment plant, where these organisms together with anammox bacteria can contribute significantly to the removal of methane and ammonium in a more sustainable way. KEY POINTS: • An enrichment culture containing both N-damo and anammox bacteria was obtained. • Simultaneous consumption of ammonia, nitrite, and methane under anoxic conditions. • In-depth metagenomic biodiversity analysis of inoculum and enrichment culture.

RevDate: 2020-07-01

Gao H, Yin X, Jiang X, et al (2020)

Diversity and spoilage potential of microbial communities associated with grape sour rot in eastern coastal areas of China.

PeerJ, 8:e9376 pii:9376.

As a polymicrobial disease, sour rot decreases grape berry yield and wine quality. The diversity of microbial communities in sour rot-affected grapes depends on the cultivation site, but the microbes responsible for this disease in eastern coastal China, has not been reported. To identify the microbes that cause sour grape rot in this important grape-producing region, the diversity and abundance of bacteria and fungi were assessed by metagenomic analysis and cultivation-dependent techniques. A total of 15 bacteria and 10 fungi were isolated from sour rot-affected grapes. High-throughput sequencing of PCR-amplicons generated from diseased grapes revealed 1343 OTUs of bacteria and 1038 OTUs of fungi. Proteobacteria and Firmicutes were dominant phyla among the 19 bacterial phyla identified. Ascomycota was the dominant fungal phylum and the fungi Issatchenkia terricola, Colletotrichum viniferum, Hanseniaspora vineae, Saprochaete gigas, and Candida diversa represented the vast majority ofmicrobial species associated with sour rot-affected grapes. An in vitro spoilage assay confirmed that four of the isolated bacteria strains (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis) and five of the isolated fungi strains (three Aspergillus species, Alternaria tenuissima, and Fusarium proliferatum) spoiled grapes. These microorganisms, which appear responsible for spoiling grapes in eastern China, appear closely related to microbes that cause this plant disease around the world.

RevDate: 2020-07-01

Neal AL, Bacq-Labreuil A, Zhang X, et al (2020)

Soil as an extended composite phenotype of the microbial metagenome.

Scientific reports, 10(1):10649 pii:10.1038/s41598-020-67631-0.

We use a unique set of terrestrial experiments to demonstrate how soil management practises result in emergence of distinct associations between physical structure and biological functions. These associations have a significant effect on the flux, resilience and efficiency of nutrient delivery to plants (including water). Physical structure, determining the air-water balance in soil as well as transport rates, is influenced by nutrient and physical interventions. Contrasting emergent soil structures exert selective pressures upon the microbiome metagenome. These selective pressures are associated with the quality of organic carbon inputs, the prevalence of anaerobic microsites and delivery of nutrients to microorganisms attached to soil surfaces. This variety results in distinctive gene assemblages characterising each state. The nature of the interactions provide evidence that soil behaves as an extended composite phenotype of the resident microbiome, responsive to the input and turnover of plant-derived organic carbon. We provide new evidence supporting the theory that soil-microbe systems are self-organising states with organic carbon acting as a critical determining parameter. This perspective leads us to propose carbon flux, rather than soil organic carbon content as the critical factor in soil systems, and we present evidence to support this view.

RevDate: 2020-07-01

Altamia MA, Lin Z, Trindade-Silva AE, et al (2020)

Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes.

mSystems, 5(3): pii:5/3/e00261-20.

Shipworms play critical roles in recycling wood in the sea. Symbiotic bacteria supply enzymes that the organisms need for nutrition and wood degradation. Some of these bacteria have been grown in pure culture and have the capacity to make many secondary metabolites. However, little is known about whether such secondary metabolite pathways are represented in the symbiont communities within their hosts. In addition, little has been reported about the patterns of host-symbiont co-occurrence. Here, we collected shipworms from the United States, the Philippines, and Brazil and cultivated symbiotic bacteria from their gills. We analyzed sequences from 22 shipworm gill metagenomes from seven shipworm species and from 23 cultivated symbiont isolates. Using (meta)genome sequencing, we demonstrate that the cultivated isolates represent all the major bacterial symbiont species and strains in shipworm gills. We show that the bacterial symbionts are distributed among shipworm hosts in consistent, predictable patterns. The symbiotic bacteria harbor many gene cluster families (GCFs) for biosynthesis of bioactive secondary metabolites, only <5% of which match previously described biosynthetic pathways. Because we were able to cultivate the symbionts and to sequence their genomes, we can definitively enumerate the biosynthetic pathways in these symbiont communities, showing that ∼150 of ∼200 total biosynthetic gene clusters (BGCs) present in the animal gill metagenomes are represented in our culture collection. Shipworm symbionts occur in suites that differ predictably across a wide taxonomic and geographic range of host species and collectively constitute an immense resource for the discovery of new biosynthetic pathways corresponding to bioactive secondary metabolites.IMPORTANCE We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis.

RevDate: 2020-07-01

Gonzalez CG, Wastyk HC, Topf M, et al (2020)

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens.

mSystems, 5(3): pii:5/3/e00200-20.

Stool-based proteomics is capable of significantly augmenting our understanding of host-gut microbe interactions. However, compared to competing technologies, such as metagenomics and 16S rRNA sequencing, it is underutilized due to its low throughput and the negative impact sample contaminants can have on highly sensitive mass spectrometry equipment. Here, we present a new stool proteomic processing pipeline that addresses these shortcomings in a highly reproducible and quantitative manner. Using this method, 290 samples from a dietary intervention study were processed in approximately 1.5 weeks, largely done by a single researcher. These data indicated a subtle but distinct monotonic increase in the number of significantly altered proteins between study participants on fiber- or fermented food-enriched diets. Lastly, we were able to classify study participants based on their diet-altered proteomic profiles and demonstrated that classification accuracies of up to 89% could be achieved by increasing the number of subjects considered. Taken together, this study represents the first high-throughput proteomic method for processing stool samples in a technically reproducible manner and has the potential to elevate stool-based proteomics as an essential tool for profiling host-gut microbiome interactions in a clinical setting.IMPORTANCE Widely available technologies based on DNA sequencing have been used to describe the kinds of microbes that might correlate with health and disease. However, mechanistic insights might be best achieved through careful study of the dynamic proteins at the interface between the foods we eat, our microbes, and ourselves. Mass spectrometry-based proteomics has the potential to revolutionize our understanding of this complex system, but its application to clinical studies has been hampered by low-throughput and laborious experimentation pipelines. In response, we developed SHT-Pro, the first high-throughput pipeline designed to rapidly handle large stool sample sets. With it, a single researcher can process over one hundred stool samples per week for mass spectrometry analysis, conservatively approximately 10× to 100× faster than previous methods, depending on whether isobaric labeling is used or not. Since SHT-Pro is fairly simple to implement using commercially available reagents, it should be easily adaptable to large-scale clinical studies.

RevDate: 2020-07-01

Leu AO, McIlroy SJ, Ye J, et al (2020)

Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae.

mBio, 11(3): pii:mBio.01325-20.

Anaerobic oxidation of methane (AOM) is an important biological process responsible for controlling the flux of methane into the atmosphere. Members of the archaeal family Methanoperedenaceae (formerly ANME-2d) have been demonstrated to couple AOM to the reduction of nitrate, iron, and manganese. Here, comparative genomic analysis of 16 Methanoperedenaceae metagenome-assembled genomes (MAGs), recovered from diverse environments, revealed novel respiratory strategies acquired through lateral gene transfer (LGT) events from diverse archaea and bacteria. Comprehensive phylogenetic analyses suggests that LGT has allowed members of the Methanoperedenaceae to acquire genes for the oxidation of hydrogen and formate and the reduction of arsenate, selenate, and elemental sulfur. Numerous membrane-bound multiheme c-type cytochrome complexes also appear to have been laterally acquired, which may be involved in the direct transfer of electrons to metal oxides, humic substances, and syntrophic partners.IMPORTANCE AOM by microorganisms limits the atmospheric release of the potent greenhouse gas methane and has consequent importance for the global carbon cycle and climate change modeling. While the oxidation of methane coupled to sulfate by consortia of anaerobic methanotrophic (ANME) archaea and bacteria is well documented, several other potential electron acceptors have also been reported to support AOM. In this study, we identify a number of novel respiratory strategies that appear to have been laterally acquired by members of the Methanoperedenaceae, as they are absent from related archaea and other ANME lineages. Expanding the known metabolic potential for members of the Methanoperedenaceae provides important insight into their ecology and suggests their role in linking methane oxidation to several global biogeochemical cycles.

RevDate: 2020-07-01

Cao H, Shimura Y, Steffen MM, et al (2020)

The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics.

mBio, 11(3): pii:mBio.01155-20.

Water bloom development due to eutrophication constitutes a case of niche specialization among planktonic cyanobacteria, but the genomic repertoire allowing bloom formation in only some species has not been fully characterized. We posited that the habitat relevance of a trait begets its underlying genomic complexity, so that traits within the repertoire would be differentially more complex in species successfully thriving in that habitat than in close species that cannot. To test this for the case of bloom-forming cyanobacteria, we curated 17 potentially relevant query metabolic pathways and five core pathways selected according to existing ecophysiological literature. The available 113 genomes were split into those of blooming (45) or nonblooming (68) strains, and an index of genomic complexity for each strain's version of each pathway was derived. We show that strain versions of all query pathways were significantly more complex in bloomers, with complexity in fact correlating positively with strain blooming incidence in 14 of those pathways. Five core pathways, relevant everywhere, showed no differential complexity or correlations. Gas vesicle, toxin and fatty acid synthesis, amino acid uptake, and C, N, and S acquisition systems were most strikingly relevant in the blooming repertoire. Further, we validated our findings using metagenomic gene expression analyses of blooming and nonblooming cyanobacteria in natural settings, where pathways in the repertoire were differentially overexpressed according to their relative complexity in bloomers, but not in nonbloomers. We expect that this approach may find applications to other habitats and organismal groups.IMPORTANCE We pragmatically delineate the trait repertoire that enables organismal niche specialization. We based our approach on the tenet, derived from evolutionary and complex-system considerations, that genomic units that can significantly contribute to fitness in a certain habitat will be comparatively more complex in organisms specialized to that habitat than their genomic homologs found in organisms from other habitats. We tested this in cyanobacteria forming harmful water blooms, for which decades-long efforts in ecological physiology and genomics exist. Our results essentially confirm that genomics and ecology can be linked through comparative complexity analyses, providing a tool that should be of general applicability for any group of organisms and any habitat, and enabling the posing of grounded hypotheses regarding the ecogenomic basis for diversification.

RevDate: 2020-07-01

Hou J, Sievert SM, Wang Y, et al (2020)

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys.

Microbiome, 8(1):102 pii:10.1186/s40168-020-00851-8.

BACKGROUND: Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys.

RESULTS: Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9-10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased.

CONCLUSIONS: This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a "fluid-shaped" microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a "mineral-shaped" community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years. Video Abstract.

RevDate: 2020-07-01

Roder T, Wüthrich D, Bär C, et al (2020)

In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes.

Microorganisms, 8(7): pii:microorganisms8070966.

The diversity of the human microbiome is positively associated with human health. However, this diversity is endangered by Westernized dietary patterns that are characterized by a decreased nutrient variety. Diversity might potentially be improved by promoting dietary patterns rich in microbial strains. Various collections of bacterial cultures resulting from a century of dairy research are readily available worldwide, and could be exploited to contribute towards this end. We have conducted a functional in silico analysis of the metagenome of 24 strains, each representing one of the species in a bacterial culture collection composed of 626 sequenced strains, and compared the pathways potentially covered by this metagenome to the intestinal metagenome of four healthy, although overweight, humans. Remarkably, the pan-genome of the 24 strains covers 89% of the human gut microbiome's annotated enzymatic reactions. Furthermore, the dairy microbial collection covers biological pathways, such as methylglyoxal degradation, sulfate reduction, g-aminobutyric (GABA) acid degradation and salicylate degradation, which are differently covered among the four subjects and are involved in a range of cardiometabolic, intestinal, and neurological disorders. We conclude that microbial culture collections derived from dairy research have the genomic potential to complement and restore functional redundancy in human microbiomes.

RevDate: 2020-07-01
CmpDate: 2020-07-01

McNair K, Zhou C, Dinsdale EA, et al (2019)

PHANOTATE: a novel approach to gene identification in phage genomes.

Bioinformatics (Oxford, England), 35(22):4537-4542.

MOTIVATION: Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present PHANOTATE, a novel method for gene calling specifically designed for phage genomes. Although the compact nature of genes in phages is a problem for current gene annotators, we exploit this property by treating a phage genome as a network of paths: where open reading frames are favorable, and overlaps and gaps are less favorable, but still possible. We represent this network of connections as a weighted graph, and use dynamic programing to find the optimal path.

RESULTS: We compare PHANOTATE to other gene callers by annotating a set of 2133 complete phage genomes from GenBank, using PHANOTATE and the three most popular gene callers. We found that the four programs agree on 82% of the total predicted genes, with PHANOTATE predicting more genes than the other three. We searched for these extra genes in both GenBank's non-redundant protein database and all of the metagenomes in the sequence read archive, and found that they are present at levels that suggest that these are functional protein-coding genes.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2020-06-30

Qian XB, Chen T, Xu YP, et al (2020)

A guide to human microbiome research: study design, sample collection, and bioinformatics analysis.

Chinese medical journal [Epub ahead of print].

The purpose of this review is to provide medical researchers, especially those without a bioinformatics background, with an easy-to-understand summary of the concepts and technologies used in microbiome research. First, we define primary concepts such as microbiota, microbiome, and metagenome. Then, we discuss study design schemes, the methods of sample size calculation, and the methods for improving the reliability of research. We emphasize the importance of negative and positive controls in this section. Next, we discuss statistical analysis methods used in microbiome research, focusing on problems with multiple comparisons and ways to compare β-diversity between groups. Finally, we provide step-by-step pipelines for bioinformatics analysis. In summary, the meticulous study design is a key step to obtaining meaningful results, and appropriate statistical methods are important for accurate interpretation of microbiome data. The step-by-step pipelines provide researchers with insights into newly developed bioinformatics analysis methods.

RevDate: 2020-06-30

New FN, IL Brito (2020)

What Is Metagenomics Teaching Us, and What Is Missed?.

Annual review of microbiology [Epub ahead of print].

Shotgun metagenomic sequencing has revolutionized our ability to detect and characterize the diversity and function of complex microbial communities. In this review, we highlight the benefits of using metagenomics as well as the breadth of conclusions that can be made using currently available analytical tools, such as greater resolution of species and strains across phyla and functional content, while highlighting challenges of metagenomic data analysis. Major challenges remain in annotating function, given the dearth of functional databases for environmental bacteria compared to model organisms, and the technical difficulties of metagenome assembly and phasing in heterogeneous environmental samples. In the future, improvements and innovation in technology and methodology will lead to lowered costs. Data integration using multiple technological platforms will lead to a better understanding of how to harness metagenomes. Subsequently, we will be able not only to characterize complex microbiomes but also able to manipulate communities to achieve prosperous outcomes for health, agriculture, and environmental sustainability. Expected final online publication date for the Annual Review of Microbiology, Volume 74 is September 8, 2020. Please see for revised estimates.

RevDate: 2020-06-30

McDowell A, McLaughlin J, AM Layton (2020)

Is Cutibacterium (previously Propionibacterium) acnes a potential pathogenic factor in the aetiology of the skin disease progressive macular hypomelanosis?.

Journal of the European Academy of Dermatology and Venereology : JEADV [Epub ahead of print].

Progressive macular hypomelanosis (PMH) is a skin condition that normally causes symmetrically distributed hypopigmented macules on the front and back of the trunk, but rarely the face. To date, the pathophysiology of the condition is not well understood, but a role for the anaerobic skin bacterium Cutibacterium (previously Propionibacterium) acnes in the development of the disease has been proposed due to its sole presence within lesional, but not normal peri-lesional, skin. The success of antimicrobials in the treatment of PMH also provides circumstantial evidence that this association may be causal, although this is still to be proven. More recent culture and metagenomic typing studies indicate that strains of C. acnes subsp. elongatum (type III) may be important in the aetiology of the condition, which would help to explain why PMH does not normally affect the face since such strains are rarely present there, and why no association between this condition and acne vulgaris is found; acne appears to primarily involve type IA1 strains from C. acnes subsp. acnes (type I). In this review we summarise current knowledge on the relationship between C. acnes and PMH, and re-examine previous challenges to the view that the bacterium plays a role in the condition against the backdrop of newly emerged data.

RevDate: 2020-06-30

Mahadevan P, ML Middlebrooks (2020)

Bacterial diversity in the clarki ecotype of the photosynthetic sacoglossan, Elysia crispata.

MicrobiologyOpen [Epub ahead of print].

Few studies have examined the bacterial communities associated with photosynthetic sacoglossan sea slugs. In this study, we determined the bacterial diversity in the clarki ecotype, Elysia crispata using 16S rRNA sequencing. Computational analysis using QIIME2 revealed variability between individual samples, with the Spirochaetes and Bacteroidetes phyla dominating most samples. Tenericutes and Proteobacteria were also found, among other phyla. Computational metabolic profiling of the bacteria revealed a variety of metabolic pathways involving carbohydrate metabolism, lipid metabolism, nucleotide metabolism, and amino acid metabolism. Although associated bacteria may be involved in mutually beneficial metabolic pathways, there was a high degree of variation in the bacterial community of individual slugs. This suggests that many of these relationships are likely opportunistic rather than obligate and that many of these bacteria may live commensally providing no major benefit to the slugs.

RevDate: 2020-06-30

Delbeke H, Younas S, Casteels I, et al (2020)

Current knowledge on the human eye microbiome: a systematic review of available amplicon and metagenomic sequencing data.

Acta ophthalmologica [Epub ahead of print].

Insights in the ocular surface microbiome are still at an early stage and many more questions remain unanswered compared with other human-associated microbial communities. The current knowledge on the human microbiome changed our viewpoint on bacteria and human health and significantly enhanced our understanding of human pathophysiology. Also in ocular medicine, microbiome research might impact treatment. Here, we summarize the current knowledge on ocular microbiome research with a particular focus on potential confounding factors and their effects on microbiome composition. Moreover, we present the ocular surface core microbiome based on current available data and defined it as genera present in almost half of the published control cohorts with a relative abundance of at least 1%.

RevDate: 2020-06-30

Starý L, Mezerová K, Vysloužil K, et al (2020)

Candida albicans culture from a rectal swab can be associated with newly diagnosed colorectal cancer.

Folia microbiologica pii:10.1007/s12223-020-00807-3 [Epub ahead of print].

Plenty of metagenomic studies have suggested possible associations between microbiome composition and colorectal cancer (CRC). However, these techniques are not economic enough for routine use so far. Therefore, we explored the possibility to detect species associated with colorectal cancer by conventional culture from rectal swab. Fifty-two patients newly diagnosed for adenoma/CRC and 52 age-matched controls were recruited and sampled. Rectal swabs were inoculated on several types of plates and incubated appropriately under both aerobic and anaerobic conditions. All colonial morphotypes were subcultured and identified using MALDI-ToF MS. Although no bacterial species was significantly associated with CRC in our study, we surprisingly observed a strong and significant overrepresentation of the yeast Candida albicans in cases (P = 0.0066, odds ratio 5.444 [95% CI 1.449-20.462]). Potential confounding factors were associated neither with CRC (history of CRC in first-degree relatives, a personal history of appendectomy and cholecystectomy, increased BMI (body mass index), and the percentage of males) nor with C. albicans presence (preexisting diabetes and PPI medication) in our cohort. A growing body of evidence supports the view that C. albicans does cause cancer in humans. We hypothesize that presence of C. albicans in the gut may induce or facilitate some part of the sporadic CRC cases. Our observation should be a strong incentive to verify the potential usefulness of the easily culturable C. albicans yeast as a screening marker for patients at risk of CRC or those suffering an early asymptomatic stage of CRC.

RevDate: 2020-06-30

Boratto PVM, Oliveira GP, Machado TB, et al (2020)

Yaravirus: A novel 80-nm virus infecting Acanthamoeba castellanii.

Proceedings of the National Academy of Sciences of the United States of America pii:2001637117 [Epub ahead of print].

Here we report the discovery of Yaravirus, a lineage of amoebal virus with a puzzling origin and evolution. Yaravirus presents 80-nm-sized particles and a 44,924-bp dsDNA genome encoding for 74 predicted proteins. Yaravirus genome annotation showed that none of its genes matched with sequences of known organisms at the nucleotide level; at the amino acid level, six predicted proteins had distant matches in the nr database. Complimentary prediction of three-dimensional structures indicated possible function of 17 proteins in total. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe. The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially representing a divergent major capsid protein (MCP) with a predicted double jelly-roll domain. Structure-guided phylogeny of MCP suggests that Yaravirus groups together with the MCPs of Pleurochrysis endemic viruses. Yaravirus expands our knowledge of the diversity of DNA viruses. The phylogenetic distance between Yaravirus and all other viruses highlights our still preliminary assessment of the genomic diversity of eukaryotic viruses, reinforcing the need for the isolation of new viruses of protists.

RevDate: 2020-06-30

Moskowitz JE, Doran AG, Lei Z, et al (2020)

Integration of genomics, metagenomics, and metabolomics to identify interplay between susceptibility alleles and microbiota in adenoma initiation.

BMC cancer, 20(1):600 pii:10.1186/s12885-020-07007-9.

BACKGROUND: Colorectal cancer (CRC) is a multifactorial disease resulting from both genetic predisposition and environmental factors including the gut microbiota (GM), but deciphering the influence of genetic variants, environmental variables, and interactions with the GM is exceedingly difficult. We previously observed significant differences in intestinal adenoma multiplicity between C57BL/6 J-ApcMin (B6-Min/J) from The Jackson Laboratory (JAX), and original founder strain C57BL/6JD-ApcMin (B6-Min/D) from the University of Wisconsin.

METHODS: To resolve genetic and environmental interactions and determine their contributions we utilized two genetically inbred, independently isolated ApcMin mouse colonies that have been separated for over 20 generations. Whole genome sequencing was used to identify genetic variants unique to the two substrains. To determine the influence of genetic variants and the impact of differences in the GM on phenotypic variability, we used complex microbiota targeted rederivation to generate two Apc mutant mouse colonies harboring complex GMs from two different sources (GMJAX originally from JAX or GMHSD originally from Envigo), creating four ApcMin groups. Untargeted metabolomics were used to characterize shifts in the fecal metabolite profile based on genetic variation and differences in the GM.

RESULTS: WGS revealed several thousand high quality variants unique to the two substrains. No homozygous variants were present in coding regions, with the vast majority of variants residing in noncoding regions. Host genetic divergence between Min/J and Min/D and the complex GM additively determined differential adenoma susceptibility. Untargeted metabolomics revealed that both genetic lineage and the GM collectively determined the fecal metabolite profile, and that each differentially regulates bile acid (BA) metabolism. Metabolomics pathway analysis facilitated identification of a functionally relevant private noncoding variant associated with the bile acid transporter Fatty acid binding protein 6 (Fabp6). Expression studies demonstrated differential expression of Fabp6 between Min/J and Min/D, and the variant correlates with adenoma multiplicity in backcrossed mice.

CONCLUSIONS: We found that both genetic variation and differences in microbiota influences the quantitiative adenoma phenotype in ApcMin mice. These findings demonstrate how the use of metabolomics datasets can aid as a functional genomic tool, and furthermore illustrate the power of a multi-omics approach to dissect complex disease susceptibility of noncoding variants.

RevDate: 2020-06-30

Yousif A, Drou N, Rowe J, et al (2020)

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization.

BMC bioinformatics, 21(1):267 pii:10.1186/s12859-020-03577-4.

BACKGROUND: As high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of many researchers. To ease this computational barrier, we have created a dynamic web-based platform, NASQAR (Nucleic Acid SeQuence Analysis Resource).

RESULTS: NASQAR offers a collection of custom and publicly available open-source web applications that make extensive use of a variety of R packages to provide interactive data analysis and visualization. The platform is publicly accessible at . Open-source code is on GitHub at , and the system is also available as a Docker image at . NASQAR is a collaboration between the core bioinformatics teams of the NYU Abu Dhabi and NYU New York Centers for Genomics and Systems Biology.

CONCLUSIONS: NASQAR empowers non-programming experts with a versatile and intuitive toolbox to easily and efficiently explore, analyze, and visualize their Transcriptomics data interactively. Popular tools for a variety of applications are currently available, including Transcriptome Data Preprocessing, RNA-seq Analysis (including Single-cell RNA-seq), Metagenomics, and Gene Enrichment.

RevDate: 2020-06-29

Zuo T, Zhan H, Zhang F, et al (2020)

Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge.

Gastroenterology pii:S0016-5085(20)34852-6 [Epub ahead of print].

BACKGROUD & AIMS: SARS-CoV-2 infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and upon recovery.

METHODS: We performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 patients with COVID-19 in Hong Kong, from February 5 through May 12, 2020. Fecal samples were collected 2 to 3 times per week from time of hospitalization until discharge. We compared fecal mycobiome compositions of patients with COVID-19 with those from 9 subjects with community-acquired pneumonia and 30 healthy individuals (controls). We assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples.

RESULTS: Patients with COVID-19 had significant alterations in their fecal mycobiomes compared with controls, characterized by enrichment of Candia albicans and a highly heterogeneous mycobiome configuration, at time of hospitalization. Although fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from those of controls during times of hospitalization, 8 of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition, through the last sample collected. The diversity of the fecal mycobiome of the last sample collected from patients with COVID-19 was 2.5-fold higher than that of controls (P<.05). Samples collected at all timepoints from patients with COVID-19 had increased proportions of opportunistic fungal pathogens, Candida albicans, Candida auris, and Aspergillus flavus compared with controls. Two respiratory-associated fungal pathogens, Aspergillus flavus and Aspergillus niger, were detected in fecal samples from a subset of patients with COVID-19, even after clearance of SARS-CoV-2 from nasopharyngeal samples and resolution of respiratory symptoms.

CONCLUSIONS: In a pilot study, we found heterogeneous configurations of the fecal mycobiome, with enrichment of fungal pathogens from the genera Candida and Aspergillus, during hospitalization of 30 patients with COVID-19 compared with controls. Unstable gut mycobiomes and prolonged dysbiosis persisted in a subset of patients with COVID-19 up to 12 days after nasopharyngeal clearance of SARS-CoV-2. Studies are needed to determine whether alterations in intestinal fungi contribute to or result from SARS-CoV-2 infection, and the effects of these changes in disease progression.

RevDate: 2020-06-29
CmpDate: 2020-06-29

Al Alam D, Danopoulos S, Grubbs B, et al (2020)

Human Fetal Lungs Harbor a Microbiome Signature.

American journal of respiratory and critical care medicine, 201(8):1002-1006.

RevDate: 2020-06-29
CmpDate: 2020-06-29

Doud DFR, Bowers RM, Schulz F, et al (2020)

Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere.

The ISME journal, 14(3):659-675.

Assigning a functional role to a microorganism has historically relied on cultivation of isolates or detection of environmental genome-based biomarkers using a posteriori knowledge of function. However, the emerging field of function-driven single-cell genomics aims to expand this paradigm by identifying and capturing individual microbes based on their in situ functions or traits. To identify and characterize yet uncultivated microbial taxa involved in cellulose degradation, we developed and benchmarked a function-driven single-cell screen, which we applied to a microbial community inhabiting the Great Boiling Spring (GBS) Geothermal Field, northwest Nevada. Our approach involved recruiting microbes to fluorescently labeled cellulose particles, and then isolating single microbe-bound particles via fluorescence-activated cell sorting. The microbial community profiles prior to sorting were determined via bulk sample 16S rRNA gene amplicon sequencing. The flow-sorted cellulose-bound microbes were subjected to whole genome amplification and shotgun sequencing, followed by phylogenetic placement. Next, putative cellulase genes were identified, expressed and tested for activity against derivatives of cellulose and xylose. Alongside typical cellulose degraders, including members of the Actinobacteria, Bacteroidetes, and Chloroflexi, we found divergent cellulases encoded in the genome of a recently described candidate phylum from the rare biosphere, Goldbacteria, and validated their cellulase activity. As this genome represents a species-level organism with novel and phylogenetically distinct cellulolytic activity, we propose the name Candidatus 'Cellulosimonas argentiregionis'. We expect that this function-driven single-cell approach can be extended to a broad range of substrates, linking microbial taxonomy directly to in situ function.

RevDate: 2020-06-29
CmpDate: 2020-06-29

Ansorge R, Romano S, Sayavedra L, et al (2019)

Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels.

Nature microbiology, 4(12):2487-2497.

Genetic diversity of closely related free-living microorganisms is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Accordingly, strain diversity is assumed to be highly restricted in intracellular bacteria associated with animals. Here, we sequenced metagenomes and metatranscriptomes of 18 Bathymodiolus mussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individual Bathymodiolus mussels. Co-occurring symbiont strains differed extensively in key functions, such as the use of energy and nutrient sources, electron acceptors and viral defence mechanisms. Most strain-specific genes were expressed, highlighting their potential to affect fitness. We show that fine-scale diversity is pervasive in Bathymodiolus sulfur-oxidizing symbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, rather than the host, feeds the symbionts.

RevDate: 2020-06-29
CmpDate: 2020-06-29

Džunková M, Low SJ, Daly JN, et al (2019)

Defining the human gut host-phage network through single-cell viral tagging.

Nature microbiology, 4(12):2192-2203.

Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host-phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then individually sorted as host-phage pairs, followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host-phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple individual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host-phage network, suggesting that phages are not major vectors of inter-species horizontal gene transfer in the human gut. A high level of cross-reactivity between phages and bacteria from different subjects was noted despite subject-specific viral profiles, which has implications for faecal microbiota transplant therapy.

RevDate: 2020-06-27

Li S, Zhao B, Jin M, et al (2020)

A comprehensive survey on the horizontal and vertical distribution of heavy metals and microorganisms in soils of a Pb/Zn smelter.

Journal of hazardous materials, 400:123255 pii:S0304-3894(20)31244-9 [Epub ahead of print].

Smelter emissions have brought serious heavy metal contamination. Comprehensive surveys of spatial heavy metal and microorganism distribution in soils of smelters aera are still limited. In this study, the horizontal and vertical profiles of heavy metals as well as microorganisms of 80 samples from 5 soil layers of 16 sites in a Pb/Zn smelter were studied. Pollution index indicated the pollution level as Cd > Zn > Pb > As > Cu > Mn > Co > Cr > V, and the severe pollutants were Cd, Zn, Pb, As and Cu. The hazard quotient and hazard index indicated that the topsoil might pose high chronic risk to children mainly due to high content of Pb, As and Cd. The whole smelter was heavily polluted even to the depth of 100 cm as revealed by Nemerow pollution indices. Depth-related microbiota analysis indicated high richness of indigenous microorganisms and significant differences in vertical microbial structure. Proteobacteria was the dominant phylum in all depth layers, followed by Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria as major phyla. pH and heavy metals Zn, Cu, As, Mn and Cd significantly influenced the microbiota composition. Metagenomic functional prediction suggested antioxidant response, metal exportation and biotransformation play roles in bio-resistance to and bioremoval of heavy metals.

RevDate: 2020-06-27

Cerqueira F, Christou A, Fatta-Kassinos D, et al (2020)

Effects of prescription antibiotics on soil- and root-associated microbiomes and resistomes in an agricultural context.

Journal of hazardous materials, 400:123208 pii:S0304-3894(20)31197-3 [Epub ahead of print].

The use of treated wastewater for crop irrigation is rapidly increasing to respond to the ever-growing demands for water and food resources. However, this practice may contribute to the spread of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in agricultural settings. To evaluate this potential risk, we analyzed microbiomes and resistomes of soil and Lactuca sativa L. (lettuce) root samples from pots irrigated with tap water spiked with 0, 20, or 100 μg L-1 of a mixture of three antibiotics (Trimethoprim, Ofloxacin, Sulfamethoxazole). The presence of antibiotics induced changes in bacterial populations, particularly in soil, as revealed by 16S rDNA sequence analysis. Parallel shotgun sequencing identified a total of 56 different ARGs conferring resistance against 14 antibiotic families. Antibiotic -treated samples showed increased loads of ARGs implicated in mutidrug resistance or in both direct and indirect acquired resistance. These changes correlated with the prevalence of Xantomonadales species in the root microbiomes. We interpret these data as indicating different strategies of soil and root microbiomes to cope with the presence of antibiotics, and as a warning that their presence may increase the loads of ARBs and ARGs in edible plant parts, therefore constituting a potential risk for human consumers.

RevDate: 2020-06-27

Wylezich C, Caccio SM, Walochnik J, et al (2020)

Untargeted metagenomics shows a reliable performance for synchronous detection of parasites.

Parasitology research pii:10.1007/s00436-020-06754-9 [Epub ahead of print].

Shotgun metagenomics with high-throughput sequencing (HTS) techniques is increasingly used for pathogen identification and characterization. While many studies apply targeted amplicon sequencing, here we used untargeted metagenomics to simultaneously identify protists and helminths in pre-diagnosed faecal and tissue samples. The approach starts from RNA and operates without an amplification step, therefore allowing the detection of all eukaryotes, including pathogens, since it circumvents the bias typically observed in amplicon-based HTS approaches. The generated metagenomics datasets were analysed using the RIEMS tool for initial taxonomic read assignment. Mapping analyses against ribosomal reference sequences were subsequently applied to extract 18S rRNA sequences abundantly present in the sequence datasets. The original diagnosis, which was based on microscopy and/or PCR, could be confirmed in nearly all cases using ribosomal RNA metagenomics. In addition to the pre-diagnosed taxa, we detected other intestinal eukaryotic parasites of uncertain pathogenicity (of the genera Dientamoeba, Entamoeba, Endolimax, Hymenolepis) that are often excluded from routine diagnostic protocols. The study clearly demonstrates the applicability of untargeted RNA metagenomics for the parallel detection of parasites.

RevDate: 2020-06-27

Luo Y, Huang Y, Xu R, et al (2020)

Primary and secondary succession mediates the accumulation of biogenic amines during industrial semidry Chinese rice wine fermentation.

Applied and environmental microbiology pii:AEM.01177-20 [Epub ahead of print].

The exogenous functional microorganisms to regulate the biogenic amines (BAs) content is a common approach in fermentation systems. Here, to better understand the microbial traits of succession trajectories in resource-based and biotic interference system, the BAs-related primary and secondary succession were tracked during industrial semidry Chinese rice wine (CRW) fermentation. Dominant abundance and BAs-associated microbial functionality based on PICRUSt indicated that Citrobacter, Acinetobacter, Lactobacillus, Exiguobacterium, Bacillus, Pseudomonas and Enterobacter were prominently contributed to decarboxylase gene family in CRW. The expression level of tyrosine decarboxylase (tyrDC), ornithine decarboxylase (odc) and agmatine deiminase gene (aguA) were assessed by q-PCR. The transcription levels of these genes are unmatched with BAs formation rate during post fermentation, indicating that acidification and carbon source depletion upregulated the expression and microbes launch the dormancy strategy to respond to unfavorable conditions. Furthermore, microbial interference of CRW fermentation by co-inoculated Lactobacillus plantarum (ACBC271) and Staphylococcus xylosus (CGMCC1.8382) at a ratio of 1:2 exhibited the best synergetic control of BAs. Spearman correlations revealed that Lactobacillus and Staphylococcus exhibited influence on BAs-associated microbiota (|ρ|>0), Exiguobacterium and Pseudomonas were strongly suppress by Lactobacillus (P < 0.05, ρ = -0.867, ρ = -0.782), Staphylococcus showed the strongest inhibitory effect toward Lactobacillus (ρ = -0.115) and Citrobacter (ρ = -0.188) in co-inoculated 1:2 group. The high inhibitory effect of exogenous added strains on specific bacteria presented the evidence for the obtained BAs-associated contributors. Overall, this work provides important insight into the microbial traits rely on resource usage and functional microbiota within food microbial ecology.Importance Understanding the shifting patterns of substance usage and microbial interactions is a fundamental objective within microbiology and ecology. Analyses of primary and secondary microbial succession allows for determinations of taxonomic diversity, community traits and functional transformations over time or after a disturbance. The kinetics of BA generation, the patterns of resource consumption, functional metagenome prediction and microbial interactions were profiled to elucidate the equilibrium mechanism of microbial systems. Secondary succession after a disturbance triggers a change in resource usage, which in turn affects primary succession and metabolism. In the study, the functional potential of exogenous microorganisms under disturbance synergized with secondary succession strategies, including rebalancing and dormancy, which ultimately lowered BA accumulation. Thus, this succession system could facilitate to settle essential issues with respect to microbial traits rely on resource usage and microbial interactions that occur in natural ecosystems.

RevDate: 2020-06-27

Leung MHY, Tong X, Bastien P, et al (2020)

Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants.

Microbiome, 8(1):100 pii:10.1186/s40168-020-00874-1.

BACKGROUND: Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous microbiota. Given the roles of the skin microbiota have on healthy and undesirable skin phenotypes and the relationships between PAHs and skin properties, we hypothesize that exposure of PAHs may be associated with changes in the cutaneous microbiota. In this study, the skin microbiota of over two hundred Chinese individuals from two cities in China with varying exposure levels of PAHs were characterized by bacterial and fungal amplicon and shotgun metagenomics sequencing.

RESULTS: Skin site and city were strong parameters in changing microbial communities and their assembly processes. Reductions of bacterial-fungal microbial network structural integrity and stability were associated with skin conditions (acne and dandruff). Multivariate analysis revealed associations between abundances of Propionibacterium and Malassezia with host properties and pollutant exposure levels. Shannon diversity increase was correlated to exposure levels of PAHs in a dose-dependent manner. Shotgun metagenomics analysis of samples (n = 32) from individuals of the lowest and highest exposure levels of PAHs further highlighted associations between the PAHs quantified and decrease in abundances of skin commensals and increase in oral bacteria. Functional analysis identified associations between levels of PAHs and abundance of microbial genes of metabolic and other pathways with potential importance in host-microbe interactions as well as degradation of aromatic compounds.

CONCLUSIONS: The results in this study demonstrated the changes in composition and functional capacities of the cutaneous microbiota associated with chronic exposure levels of PAHs. Findings from this study will aid the development of strategies to harness the microbiota in protecting the skin against pollutants. Video Abstract.

RevDate: 2020-06-27

Liu J, Zhu Y, Jay-Russell M, et al (2020)

Reservoirs of antimicrobial resistance genes in retail raw milk.

Microbiome, 8(1):99 pii:10.1186/s40168-020-00861-6.

BACKGROUND: It has been estimated that at least 3% of the USA population consumes unpasteurized (raw) milk from animal sources, and the demand to legalize raw milk sales continues to increase. However, consumption of raw milk can cause foodborne illness and be a source of bacteria containing transferrable antimicrobial resistance genes (ARGs). To obtain a comprehensive understanding of the microbiome and antibiotic resistome in both raw and processed milk, we systematically analyzed 2034 retail milk samples including unpasteurized milk and pasteurized milk via vat pasteurization, high-temperature-short-time pasteurization, and ultra-pasteurization from the United States using complementary culture-based, 16S rRNA gene, and metagenomic sequencing techniques.

RESULTS: Raw milk samples had the highest prevalence of viable bacteria which were measured as all aerobic bacteria, coliform, and Escherichia coli counts, and their microbiota was distinct from other types of milk. 16S rRNA gene sequencing revealed that Pseudomonadaceae dominated raw milk with limited levels of lactic acid bacteria. Among all milk samples, the microbiota remained stable with constant bacterial populations when stored at 4 °C. In contrast, storage at room temperature dramatically enriched the bacterial populations present in raw milk samples and, in parallel, significantly increased the richness and abundance of ARGs. Metagenomic sequencing indicated raw milk possessed dramatically more ARGs than pasteurized milk, and a conjugation assay documented the active transfer of blaCMY-2, one ceftazidime resistance gene present in raw milk-borne E. coli, across bacterial species. The room temperature-enriched resistome differed in raw milk from distinct geographic locations, a difference likely associated with regionally distinct milk microbiota.

CONCLUSION: Despite advertised "probiotic" effects, our results indicate that raw milk microbiota has minimal lactic acid bacteria. In addition, retail raw milk serves as a reservoir of ARGs, populations of which are readily amplified by spontaneous fermentation. There is an increased need to understand potential food safety risks from improper transportation and storage of raw milk with regard to ARGs. Video Abstract.

RevDate: 2020-06-27

Wu S, Zhou L, Zhou Y, et al (2020)

Diverse and unique viruses discovered in the surface water of the East China Sea.

BMC genomics, 21(1):441 pii:10.1186/s12864-020-06861-y.

BACKGROUND: Viruses are the most abundant biological entities on earth and play import roles in marine biogeochemical cycles. Here, viral communities in the surface water of the East China Sea (ECS) were collected from three representative regions of Yangshan Harbor (YSH), Gouqi Island (GQI), and the Yangtze River Estuary (YRE) and explored primarily through epifluorescence microscopy (EM), transmission electron microscopy (TEM), and metagenomics analysis.

RESULTS: The virus-like particles (VLPs) in the surface water of the ECS were measured to be 106 to 107 VLPs/ml. Most of the isolated viral particles possessed a head-and-tail structure, but VLPs with unique morphotypes that had never before been observed in the realm of viruses were also found. The sequences related to known viruses in GenBank accounted for 21.1-22.8% of the viromic datasets from YSH, GQI, and YRE. In total, 1029 viral species were identified in the surface waters of the ECS. Among them, tailed phages turn out to make up the majority of viral communities, however a small number of Phycodnaviridae or Mimiviridae related sequences were also detected. The diversity of viruses did not appear to be a big difference among these three aquatic environments but their relative abundance was geographically variable. For example, the Pelagibacter phage HTVC010P accounted for 50.4% of the identified viral species in GQI, but only 9.1% in YSH and 11.7% in YRE. Sequences, almost identical to those of uncultured marine thaumarchaeal dsDNA viruses and magroviruses that infect Marine Group II Euryarchaeota, were confidently detected in the ECS viromes. The predominant classes of virome ORFs with functional annotations that were found were those involved in viral biogenesis. Virus-host connections, inferred from CRISPR spacer-protospacer mapping, implied newly discovered infection relationships in response to arms race between them.

CONCLUSIONS: Together, both identified viruses and unknown viral assemblages observed in this study were indicative of the complex viral community composition found in the ECS. This finding fills a major gap in the dark world of oceanic viruses of China and additionally contributes to the better understanding of global marine viral diversity, composition, and distribution.

RevDate: 2020-06-26

Zhang G, Guan Y, Zhao R, et al (2020)

Metagenomic and network analyses decipher profiles and co-occurrence patterns of antibiotic resistome and bacterial taxa in the reclaimed wastewater distribution system.

Journal of hazardous materials, 400:123170 pii:S0304-3894(20)31159-6 [Epub ahead of print].

Metagenomic and network analyses were applied to decipher the profiles and co-occurrence of resistome and microbial taxa in the reclaimed wastewater distribution system, including reclaimed wastewater and two types of biofilms, i.e., surface layer biofilms and inner layer biofilms. The effects of chlorination, UV irradiation and no disinfection treatment on ARG relative abundance and composition were systemically investigated. The reclaimed wastewater possesses more diverse and abundant ARGs than biofilms and total ARG relative abundance followed the order of reclaimed wastewater samples > surface layer biofilms > inner layer biofilms. Multidrug, bacitracin, sulfonamide, aminoglycoside, beta-lactam, and macrolide-lincosamide-streptogramin resistance genes were the six most dominant ARG types and their sum accounted for 90.1 %-96.0 % of the total ARG relative abundance in different samples. Beta-lactam resistance gene was the discriminative ARG type for reclaimed wastewater. Bacitracin resistance gene and bacA were the discriminative ARG type and subtype for biofilms. Chlorination significantly reduced ARG relative abundance in the reclaimed wastewater. Nevertheless, it could not reduce ARG relative abundance in biofilms. Regarding to the total ARG profiles, there were no obvious increasing or decreasing trends over time during one year period. Co-occurrence results revealed twenty-six genera were deduced as the potential hosts of twenty-two ARG subtypes.

RevDate: 2020-06-26

van Zeggeren IE, Edridge AWD, van de Beek D, et al (2020)

Diagnostic accuracy of Vidisca-Ngs In patients with suspected central nervous system infections.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases pii:S1198-743X(20)30353-0 [Epub ahead of print].

OBJECTIVES: Confirming the diagnosis in viral central nervous system (CNS) infections can be difficult with current available diagnostic tools. Virus discovery cDNA-AFLP next generation sequencing (VIDISCA-NGS) is a promising viral metagenomic technique, which enables detection of all viruses in a single assay. We performed a retrospective study on diagnostic accuracy of VIDISCA-NGS in cerebrospinal fluid (CSF) of patients with suspected CNS infections.

METHODS: Consecutive adult patients presenting to the Emergency Department or inpatients, who underwent a lumbar puncture for the suspicion of a CNS infection, were included if 1) they were diagnosed with a viral CNS infection, or 2) a viral CNS infection was initially suspected but eventually a different diagnosis was made. A qPCR panel of the most common causative viruses was performed on CSF of these patients as reference standard and compared to the results of VIDISCA-NGS, the index test.

RESULTS: We included 38 patients with viral CNS infections and 35 presenting with suspected CNS infection for whom an alternative aetiology was finally established. Overall sensitivity and specificity was 52% (95% CI 31-73%) and 100% (95% CI 91-100%), respectively. One enterovirus, detected by VIDISCA-NGS, was only identified by qPCR upon retesting. Additional viruses identified by VIDISCA-NGS consisted of GB virus C, human papilloma virus, human mastadenovirus C, Merkel cell polyoma virus and anelloviruses.

CONCLUSION: In patients for whom routine diagnostics do not yield a causative pathogen, VIDISCA-NGS can be of additional value as it can detect a broader range of viruses, but it does not perform well enough to replace qPCR.

RevDate: 2020-06-26

Solbach P, Chhatwal P, Woltemate S, et al (2020)

Microbiota-associated risk factors for C. difficile acquisition in hospitalized patients: A prospective, multicentric study.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America pii:5863409 [Epub ahead of print].

BACKGROUND: Asymptomatic C. difficile colonization is believed to predispose to subsequent C. difficile infection (CDI). While emerging insights into the role of the commensal microbiota in mediating colonization resistance against C. difficile have associated CDI with specific microbial components, corresponding prospectively collected data on colonization with C. difficile are largely unavailable.

METHODS: C. difficile status was assessed by GDH EIA and real-time PCR targeting the toxin A (tcdA) and B (tcdB) genes. 16S V3 and V4 gene sequencing results from fecal samples of patients tested positive for C. difficile were analyzed by assessing alpha and beta diversity, LefSe, and the Piphillin functional inference approach to estimate functional capacity.

RESULTS: 1506 patients were recruited into a prospective observational study (DRKS00005335) upon admission into one of five academic hospitals. 936 of them provided fecal samples on admission and at discharge and were thus available for longitudinal analysis. Upon hospital admission, 5.5% (83/1506) and 3.7% (56/1506) of patients were colonized with toxigenic (TCD) and non-toxigenic C. difficile (NTCD), respectively. During hospitalization, 1.7% (16/936) acquired TCD. Risk factors for acquisition of TCD included pre-existing lung diseases, lower GI endoscopy and antibiotics. Species protecting against hospital-related C. difficile acquisition included Gemmiger spp., Odoribacter splanchnicus, Ruminococcus bromii and other Ruminococcus spp.. Metagenomic pathway analysis identified steroid biosynthesis as the most underrepresented metabolic pathway in patients who later acquire C. difficile colonization.

CONCLUSIONS: Gemmiger spp., Odoribacter splanchnicus, Ruminococcus bromii and other Ruminococci were associated with a decreased risk of C. difficile acquisition.

RevDate: 2020-06-26

Ajene IJ, Khamis FM, van Asch B, et al (2020)

Microbiome diversity in Diaphorina citri populations from Kenya and Tanzania shows links to China.

PloS one, 15(6):e0235348 pii:PONE-D-20-04601.

The Asian citrus psyllid (Diaphorina citri) is a key pest of Citrus spp. worldwide, as it acts as a vector for "Candidatus Liberibacter asiaticus (Las)", the bacterial pathogen associated with the destructive Huanglongbing (HLB) disease. Recent detection of D. citri in Africa and reports of Las-associated HLB in Ethiopia suggest that the citrus industry on the continent is under imminent threat. Endosymbionts and gut bacteria play key roles in the biology of arthropods, especially with regards to vector-pathogen interactions and resistance to antibiotics. Thus, we aim to profile the bacterial genera and to identify antibiotic resistance genes within the microbiome of different populations worldwide of D. citri. The metagenome of D. citri was sequenced using the Oxford Nanopore full-length 16S metagenomics protocol, and the "What's in my pot" (WIMP) analysis pipeline. Microbial diversity within and between D. citri populations was assessed, and antibiotic resistance genes were identified using the WIMP-ARMA workflow. The most abundant genera were key endosymbionts of D. citri ("Candidatus Carsonella", "Candidatus Profftella", and Wolbachia). The Shannon diversity index showed that D. citri from Tanzania had the highest diversity of bacterial genera (1.92), and D. citri from China had the lowest (1.34). The Bray-Curtis dissimilarity showed that China and Kenya represented the most diverged populations, while the populations from Kenya and Tanzania were the least diverged. The WIMP-ARMA analyses generated 48 CARD genes from 13 bacterial species in each of the populations. Spectinomycin resistance genes were the most frequently found, with an average of 65.98% in all the populations. These findings add to the knowledge on the diversity of the African D. citri populations and the probable introduction source of the psyllid in these African countries.

RevDate: 2020-06-26

Filipic B, Novovic K, Studholme DJ, et al (2020)

Shotgun metagenomics reveals differences in antibiotic resistance genes among bacterial communities in Western Balkans glacial lakes sediments.

Journal of water and health, 18(3):383-397.

Long-term overuse of antibiotics has driven the propagation and spreading of antibiotic resistance genes (ARGs) such as efflux pumps in the environment, which can be transferred to clinically relevant pathogens. This study explored the abundance and diversity of ARGs and mobile genetic elements within bacterial communities from sediments of three Western Balkans glacial lakes: Plav Lake (high impact of human population), Black Lake (medium impact of human population) and Donje Bare Lake (remote lake, minimal impact of human population) via shotgun metagenomics. Assembled metagenomic sequences revealed that Resistance-Nodulation-Division (RND) efflux pumps genes were most abundant in metagenome from the Plav Lake. The Integron Finder bioinformatics tool detected 38 clusters of attC sites lacking integron-integrases (CALIN) elements: 20 from Plav Lake, four from Black Lake and 14 from Donje Bare Lake. A complete integron sequence was recovered only from the assembled metagenome from Plav Lake. Plasmid contents within the metagenomes were similar, with proportions of contigs being plasmid-related: 1.73% for Plav Lake, 1.59% for Black Lake and 1.64% for Donje Bare Lake. The investigation showed that RNDs and mobile genetic elements content correlated with human population impact.

RevDate: 2020-06-26

Wang S, Breslawec AP, Li C, et al (2020)

A Colorimetric Assay to Enable High-Throughput Identification of Biofilm Exopolysaccharide-Hydrolyzing Enzymes.

Chemistry (Weinheim an der Bergstrasse, Germany) [Epub ahead of print].

Glycosidase enzymes that hydrolyze the biofilm exopolysaccharide poly-ß-(1,6)-N-acetylglucosamine (PNAG) are critical tools to study biofilm and potential therapeutic biofilm dispersal agents. Function-driven metagenomic screening is a powerful approach for discovery of new glycosidase but requires sensitive assays capable of distinguishing between the desired enzyme and functionally related enzymes. Here, we report the synthesis of a colorimetric PNAG disaccharide analog whose hydrolysis by PNAG glycosidases results in production of para-nitroaniline that can be continuously monitored at 410 nm. The assay is specific for enzymes capable of hydrolyzing PNAG and not related ß-hexosaminidase enzymes with alternative glycosidic linkage specificities. This analog enabled development of a continuous colorimetric assay for detection of PNAG hydrolyzing enzyme activity in crude E. coli cell lysates and suggest that this disaccharide probe will be critical for establishing the functional screening of metagenomic DNA libraries.

RevDate: 2020-06-26

Schoster A, Weese JS, Gerber V, et al (2020)

Dysbiosis is not present in horses with fecal water syndrome when compared to controls in spring and autumn.

Journal of veterinary internal medicine [Epub ahead of print].

BACKGROUND: Fecal water syndrome (FWS) is long-standing and common in horses, particularly in central Europe. No large epidemiological data sets exist, and the cause remains elusive. Dysbiosis could play a role in pathogenesis.

OBJECTIVES: To evaluate whether dysbiosis is present in horses with FWS when compared to stable-matched control horses in spring and autumn.

ANIMALS: Fecal samples were collected from horses with FWS (n = 16; 9 mares, 7 geldings) and controls (n = 15; 8 mares, 7 geldings).

METHODS: The bacterial microbiome of samples collected in spring and autumn of 2016 was analyzed using high-throughput sequencing. Differences in relative abundance of bacterial taxa, alpha diversity, and beta diversity indices were assessed between horses with FWS and controls based on season.

RESULTS: Differences in microbial community composition based on time point and health status were not observed on any taxonomic level. Limited differences were seen on linear discriminant analysis effect size analysis. No difference in alpha diversity indices was observed including richness, diversity based on health status, or time point. No effect of health status on microbial community membership structure was observed.

Limited differences were found in the bacterial microbiota of horses with and without FWS, regardless of season. Further research is needed to elucidate the role of microbiota in the development of FWS.

RevDate: 2020-06-26

Zambounis A, Ganopoulos I, Tsaftaris A, et al (2020)

Metagenomics analysis of fungal communities associated with postharvest diseases in pear fruits under the effect of management practices.

Archives of microbiology pii:10.1007/s00203-020-01960-6 [Epub ahead of print].

An amplicon metagenomic approach based on the ITS1 region of fungal rDNA was employed to identify the composition of fungal communities associated with diseases of pear fruits during postharvest storage. The sampled fruits were harvested at an orchard using routine management practices involving treatments with various chemical fungicides and were transferred to a storage packinghouse. Effective tags of reading sequences clustered into 53 OTUs whereas Ascomycota was the dominant phylum (83.4%) followed by Basidiomycota (15.8%). Our results revealed that four genera, Penicillium, Rhodotorula, Alternaria and Cladosporium were the most abundant representing 59-95% of the relative abundance per sample. The interruption of chemical treatments during the last month before harvest altered the structure of the fungal community of fruits among untreated and treated samples, mainly in cases of relative abundance of Penicillium and Rhodotorula genera. We hypothesize that various antagonistic interactions might occur on fruit surfaces among the detected fungal genera whose relative abundances were affected by fungicide treatments. Interestingly, some common pre- and postharvest pear fungal pathogens were either less present (such as Moniliana), or undetected (such as Aspergillus, Venturia and Septoria) in untreated and treated samples.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
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Bellingham, WA 98226

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Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )