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Bibliography on: Metagenomics

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ESP: PubMed Auto Bibliography 18 Oct 2019 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: 2019-10-17

Whitfill T, J Oh (2019)

Recoding the metagenome: microbiome engineering in situ.

Current opinion in microbiology, 50:28-34 pii:S1369-5274(19)30058-X [Epub ahead of print].

Synthetic biology has enabled a new generation of tools for engineering the microbiome, including targeted antibiotics, protein delivery, living biosensors and diagnostics, and metabolic factories. Here, we discuss opportunities and limitations in microbiome engineering, focusing on a new generation of tools for in situ genetic modification of a microbiome that hold particular promise in circumventing these limitations.

RevDate: 2019-10-17

Zou M, Jie Z, Cui B, et al (2019)

Fecal microbiota transplantation results in bacterial strain displacement in patients with inflammatory bowel diseases.

FEBS open bio [Epub ahead of print].

Fecal microbiota transplantation (FMT), which is thought to have the potential to correct dysbiosis of gut microbiota, has been used to treat inflammatory bowel disease (IBD) for almost a decade. Here, we report an interventional prospective cohort study performed to elucidate the extent of and processes underlying microbiota engraftment in IBD patients after FMT treatment. The cohort included two categories of patients: (1) patients with moderate to severe Crohn's disease (CD)(Harvey-Bradshaw Index ≥ 7, n = 11) and (2) patients with ulcerative colitis (UC) (Montreal classification S2 and S3, n = 4). All patients were treated with a single FMT (via mid-gut, from healthy donors) and follow-up visits were performed at baseline, 3 days, one week, and one month after FMT (missing time points included). At each follow-up time point, fecal samples and clinical metadata were collected. For comparative analysis, 10 fecal samples from 10 healthy donors were included to represent the diversity level of normal gut microbiota. Additionally, the metagenomic data of 25 fecal samples from 5 individuals with metabolic syndrome who underwent autologous FMT treatment were downloaded from a previous published paper to represent fluctuations in microbiota induced during FMT. All fecal samples underwent shotgun metagenomic sequencing. We found that 3 days after FMT, 11 out of 15 recipients were in remission (3 out of 4 UC recipients; 8 out of 11 CD recipients). Generally, bacterial colonization was observed to be lower in CD recipients than in UC recipients at both species and strain levels. Furthermore, across species, different strains displayed disease-specific displacement advantages under two-disease status. Finally, most post-FMT species (> 80%) could be properly predicted (AUC > 85%) using a random forest classification model, with the gut microbiota composition and clinical parameters of pre-FMT recipients acting as factors that contribute to prediction accuracy.

RevDate: 2019-10-17

Yue S, Zhao D, Peng C, et al (2019)

Effects of theabrownin on serum metabolites and gut microbiome in rats with a high-sugar diet.

Food & function [Epub ahead of print].

Evidence has proven that the gut microbiota is an important environmental factor contributing to obesity by altering host energy harvest and storage. We performed a high-throughput 16S rDNA sequencing association study and serum metabolomics profiling in rats with a high-sugar diet. Our studies revealed that the high sugar diet reduced the diversity of cecal microorganisms, while the combination of theabrownin and the high sugar diet increased the diversity of cecal microorganisms and promoted reproduction of Alloprevotella, Coprostanoligenes_group, Bacteroides, Prevotellaceae_NK3B31_group, Desulfovibrio, Intestinimonas, Alistipes, Bifidobacterium, Phascolarctobacterium, Ruminococcaceae_UCG-010 and Staphylococcus. The combination also inhibited the growth of Lactobacillus, Prevotellaceae_Ga6A1_group and Tyzzerella. The Firmicutes/Bacteroidetes (F/B) ratio can be significantly reduced after the intervention of theabrownin in high sugar diet rats, and the reproduction of Bacteroides acidifaciens (BA) and Staphylococcus saprophyticus subsp. saprophyticus can be promoted. We found that the obesity-associated gut microbial species were linked to the changes in circulating metabolites. Serum levels of deoxycholic acid, cholic acid, 1H-indole-3-acetic acid, 3-indole acrylic acid and melatonin were negatively correlated with BA and Staphylococcus saprophyticus subsp. saprophyticus, but positively correlated with Lactobacillus murinus, Leptum and Gut_metagenome. 2-Hydroxy-6-methylpyridin-3-carboxylic acid, l-homoserine, and 1,7-dimethylxanthine were positively correlated with BA and Staphylococcus saprophyticus subsp. saprophyticus, but negatively correlated with Lactobacillus murinus, Leptum, and Gut_metagenome. In a high sugar diet mode, theabrownin reduced the body weight and triglycerides and improved insulin resistance mainly by targeting the reproduction of intestinal microorganisms such as BA, Staphylococcus saprophyticus subsp. saprophyticus, Lactobacillus murinus, Leptum, Gut_metagenome and so on. A strong correlation between cecal microorganisms and serum metabolites, obesity and insulin resistance was observed. Theabrownin has high potential in reducing the risk of cardiovascular diseases such as diabetes and obesity.

RevDate: 2019-10-17

Singh H, Torralba MG, Moncera KJ, et al (2019)

Gastro-intestinal and oral microbiome signatures associated with healthy aging.

GeroScience pii:10.1007/s11357-019-00098-8 [Epub ahead of print].

The human oral and gut microbiomes influence health via competition for a distinct niche in the body with pathogens, via metabolic capabilities that increase host digestive capacity and generate compounds engaged in signaling pathways and modulation of immune system functions. Old age alters our metabolic and regenerative capacity. Following recruitment of 65 human subjects in the age range of 70 to 82, we discerned healthy aging (HA) and non-healthy aging (NHA) cohorts discordant in the occurrence of one or more major diseases: (1) cancer, (2) acute or chronic cardiovascular diseases, (3) acute or chronic pulmonary diseases, (4) diabetes, and (5) stroke or neurodegenerative disorders. We analyzed these cohorts' oral microbiomes (saliva) and gut microbiomes (stool) to assess diversity and identify microbial biomarkers for HA. In contrast to the gut microbiome where no change was observed, we found that the saliva microbiome had higher α-diversity in the HA compared with the NHA group. We observed the genus Akkermansia to be significantly more abundant in the gut microbiota of the HA group. Akkermansia muciniphila is a colonic mucin-degrading bacterium believed to have beneficial effects on gastrointestinal health, particularly in the context of diabetes and obesity. Erysipelotrichaceae UCG-003 was a taxon increased in abundance in the HA cohort. Streptococcus was the only genus observed to be significantly decreased in abundance in both the gut and oral microbiomes of the HA cohort compared with the NHA cohort. Our data support the notion that these microbes are potential probiotics to decrease the risks of non-healthy aging.

RevDate: 2019-10-17

Bal A, Oriol G, Josset L, et al (2019)

Metagenomic Investigation of Torque Teno Mini Virus-SH in Hematological Patients.

Frontiers in microbiology, 10:1898.

A new member of Anelloviridae, named torque teno mini virus (TTMV)-SH, was recently identified in the serum of three Hodgkin's lymphoma patients suggesting that TTMV-SH may be associated with this type of hematological malignancy. We investigated by metagenomic analysis the presence of TTMV-SH-related viruses in plasma samples (n = 323) collected from patients with various hematological malignancies (multiple myeloma (MM, n = 256), non-Hodgkin's lymphoma (NHL, n = 20), acute myeloid leukemia (n = 10)) and from healthy donors (n = 37). TTMV-SH-related strains were identified in 24 samples corresponding to four MM and one NHL patients. Phylogenic analysis revealed that the 24 isolates were close to the TTMV-SH strains previously identified, sharing 79.6-86.7% ORF1 nucleotide sequence identity. These results suggest that TTMV-SH-related viruses might be found in hematological diseases other than Hodgkin's lymphoma. Due to the high genetic variability within Anelloviridae species, the association between a particular medical condition and a new genotype should be interpreted with caution.

RevDate: 2019-10-17

Miller S, Chiu C, Rodino KG, et al (2019)

Should we be performing metagenomic next-generation sequencing for infectious disease diagnosis in the clinical laboratory?.

Journal of clinical microbiology pii:JCM.01739-19 [Epub ahead of print].

With established applications of next-generation sequencing in inherited diseases and oncology, clinical laboratories are evaluating the use of metagenomics for identification of infectious agents directly from patient samples to aid in the diagnosis of infections.….

RevDate: 2019-10-17

Petersen LM, Martin IW, Moschetti WE, et al (2019)

Third generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing.

Journal of clinical microbiology pii:JCM.01315-19 [Epub ahead of print].

Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, length of time to results, and need for technical and bioinformatics expertise. However, the recent technological innovation of nanopore sequencing from Oxford Nanopore Technologies (ONT) has the potential to address these challenges. ONT sequencing is an attractive platform for clinical laboratories to adopt due to its low cost, rapid turnaround time, and user-friendly bioinformatics pipelines. Yet it still faces the problem of base-calling accuracy as compared to other platforms. This review highlights the general challenges of pathogen detection in clinical specimens by metagenomic sequencing, the advantages and disadvantages of the ONT platform, and how research to date supports the potential future use of nanopore sequencing in infectious disease diagnostics.

RevDate: 2019-10-17

Elokil AA, Magdy M, Melak S, et al (2019)

Faecal microbiome sequences in relation to the egg-laying performance of hens using amplicon-based metagenomic association analysis.

Animal : an international journal of animal bioscience pii:S1751731119002428 [Epub ahead of print].

Exploring the composition and structure of the faecal microbial community improves the understanding of the role of the gut microbiota in the gastrointestinal function and the egg-laying performance of hens. Therefore, detection of hen-microbial interactions can explore a new breeding marker for the selection of egg production due to the important role of the gut microbiome in the host's metabolism and health. Recently, the gut microbiota has been recognised as a regulator of host performance, which has led to investigations of the productive effects of changes in the faecal microbiome in various animals. In the present study, a metagenomics analysis was applied to characterise the composition and structural diversity of faecal microbial communities under two selections of egg-laying performance, high (H, n = 30) and low (L, n = 30), using 16S rRNA-based metagenomic association analysis. The most abundant bacterial compositions were estimated based on the operational classification units among samples and between the groups from metagenomic data sets. The results indicated that Firmicutes phylum has higher significant (P < 0.01) in the H group than in the L group. In addition, higher relative abundance phyla of Bacteroides and Fusobacteria were estimated in the H group than the L group, contrasting the phyla of Actinobacteria, Cyanobacteria and Proteobacteria were more relative abundance in the L group. The families (Lactobacillus, Bifidobacterium, Acinetobacter, Flavobacteriaceae, Lachnoclostridum and Rhodococcus) were more abundant in the H group based on the comparison between the H and L groups. Meanwhile, three types of phyla (Proteobacteria, Actinobacteria and Cyanobacteria) and six families (Acinetobacter, Avibacterium, Clostridium, Corynebacterium, Helicobacter and Peptoclostridium) were more abundant in the L group (P < 0.01). Overall, the selection of genotypes has enriched a relationship between the gut microbiota and the egg-laying performance. These findings suggest that the faecal microbiomes of chickens with high egg-laying performance have more diverse activities than those of chickens with low egg-laying performance, which may be related to the metabolism and health of the host and egg production variation.

RevDate: 2019-10-16

Wang C, Schaefer L, Bian F, et al (2019)

Dysbiosis Modulates Ocular Surface Inflammatory Response to Liposaccharide.

Investigative ophthalmology & visual science, 60(13):4224-4233.

Purpose: The purpose of this study was to investigate the inflammatory response of cornea and conjunctiva to topically applied lipopolysaccharide (LPS) in mice with and without antibiotic (antibiotic cocktail, ABX) induced dysbiosis.

Methods: Dysbiosis was induced by oral antibiotics for 14 days in a group of conventional female C57BL/6J (B6) mice. 16S rRNA sequencing investigated microbiome composition. Intestinal microbiome differences were assessed using 16S rRNA sequencing of fecal pellet DNA. Blood was collected after euthanasia. CD86 expression in draining nodes was examined by flow cytometry. At day 15, a single dose of LPS or vehicle was topically applied to ABX and naïve mice. Corneal epithelium and conjunctiva were obtained after 4 hours and processed for gene expression analysis. A separate group of germ-free (GF) B6 mice was also topically challenged with LPS.

Results: Antibiotic treatment significantly decreased intestinal diversity and increased serum levels of LPS. This was accompanied by a significant increase in CD86+MHC II+CD11c+CD11b+ cells in draining nodes. Compared to vehicle, topically applied LPS increased IL-1β, TNF-α, and CXCL10 mRNA transcripts in cornea and IL-1β, TNF-α, and CXCL10 in the conjunctiva in conventional and antibiotic-treated groups. However, there was higher TNF-α, CXCL10, and IL-12 expression in the cornea of LPS-treated ABX mice compared to LPS-treated mice with intact microbiota. LPS stimulation on GF conjunctiva mirrored the results in ABX mice, although greater IL-12 and IFN-γ expression was observed in GF conjunctiva compared to conventional LPS-treated mice.

Conclusions: Acute depletion of commensals through antibiotics or germ-free environment worsens the inflammatory response to LPS.

RevDate: 2019-10-16

Saborío-Montero A, Gutiérrez-Rivas M, García-Rodríguez A, et al (2019)

Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie [Epub ahead of print].

The advent of metagenomics in animal breeding poses the challenge of statistically modelling the relationship between the microbiome, the host genetics and relevant complex traits. A set of structural equation models (SEMs) of a recursive type within a Markov chain Monte Carlo (MCMC) framework was proposed here to jointly analyse the host-metagenome-phenotype relationship. A non-recursive bivariate model was set as benchmark to compare the recursive model. The relative abundance of rumen microbes (RA), methane concentration (CH4) and the host genetics was used as a case of study. Data were from 337 Holstein cows from 12 herds in the north and north-west of Spain. Microbial composition from each cow was obtained from whole metagenome sequencing of ruminal content samples using a MinION device from Oxford Nanopore Technologies. Methane concentration was measured with Guardian® NG infrared gas monitor from Edinburgh Sensors during cow's visits to the milking automated system. A quarterly average from the methane eructation peaks for each cow was computed and used as phenotype for CH4 . Heritability of CH4 was estimated at 0.12 ± 0.01 in both the recursive and bivariate models. Likewise, heritability estimates for the relative abundance of the taxa overlapped between models and ranged between 0.08 and 0.48. Genetic correlations between the microbial composition and CH4 ranged from -0.76 to 0.65 in the non-recursive bivariate model and from -0.68 to 0.69 in the recursive model. Regardless of the statistical model used, positive genetic correlations with methane were estimated consistently for the seven genera pertaining to the Ciliophora phylum, as well as for those genera belonging to the Euryarchaeota (Methanobrevibacter sp.), Chytridiomycota (Neocallimastix sp.) and Fibrobacteres (Fibrobacter sp.) phyla. These results suggest that rumen's whole metagenome recursively regulates methane emissions in dairy cows and that both CH4 and the microbiota compositions are partially controlled by the host genotype.

RevDate: 2019-10-16

Kolb M, Lazarevic V, Emonet S, et al (2019)

Next-Generation Sequencing for the Diagnosis of Challenging Culture-Negative Endocarditis.

Frontiers in medicine, 6:203.

Diagnosis of culture-negative infective endocarditis usually implies indirect pathogen identification by serologic or molecular techniques. Clinical metagenomics, relying on next-generation sequencing (NGS) is an emerging approach that allows pathogen identification in challenging situations, as evidenced by a clinical case. We sequenced the DNA extracted from the surgically-removed frozen valve tissue from a patient with suspected infective endocarditis with negative blood and valve cultures. Mapping of the sequence reads against reference genomic sequences, a 16S rRNA gene database and clade-specific marker genes suggested an infection caused by Cardiobacterium hominis.

RevDate: 2019-10-16

Srivastava D, Baksi KD, Kuntal BK, et al (2019)

"EviMass": A Literature Evidence-Based Miner for Human Microbial Associations.

Frontiers in genetics, 10:849.

The importance of understanding microbe-microbe as well as microbe-disease associations is one of the key thrust areas in human microbiome research. High-throughput metagenomic and transcriptomic projects have fueled discovery of a number of new microbial associations. Consequently, a plethora of information is being added routinely to biomedical literature, thereby contributing toward enhancing our knowledge on microbial associations. In this communication, we present a tool called "EviMass" (Evidence based mining of human Microbial Associations), which can assist biologists to validate their predicted hypotheses from new microbiome studies. Users can interactively query the processed back-end database for microbe-microbe and disease-microbe associations. The EviMass tool can also be used to upload microbial association networks generated from a human "disease-control" microbiome study and validate the associations from biomedical literature. Additionally, a list of differentially abundant microbes for the corresponding disease can be queried in the tool for reported evidences. The results are presented as graphical plots, tabulated summary, and other evidence statistics. EviMass is a comprehensive platform and is expected to enable microbiome researchers not only in mining microbial associations, but also enriching a new research hypothesis. The tool is available free for academic use at

RevDate: 2019-10-16

Chevrette MG, Carlos-Shanley C, Louie KB, et al (2019)

Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces.

Frontiers in microbiology, 10:2170.

The advent of culture independent approaches has greatly facilitated insights into the vast diversity of bacteria and the ecological importance they hold in nature and human health. Recently, metagenomic surveys and other culture-independent methods have begun to describe the distribution and diversity of microbial metabolism across environmental conditions, often using 16S rRNA gene as a marker to group bacteria into taxonomic units. However, the extent to which similarity at the conserved ribosomal 16S gene correlates with different measures of phylogeny, metabolic diversity, and ecologically relevant gene content remains contentious. Here, we examine the relationship between 16S identity, core genome divergence, and metabolic gene content across the ancient and ecologically important genus Streptomyces. We assessed and quantified the high variability of average nucleotide identity (ANI) and ortholog presence/absence within Streptomyces, even in strains identical by 16S. Furthermore, we identified key differences in shared ecologically important characters, such as antibiotic resistance, carbohydrate metabolism, biosynthetic gene clusters (BGCs), and other metabolic hallmarks, within 16S identities commonly treated as the same operational taxonomic units (OTUs). Differences between common phylogenetic measures and metabolite-gene annotations confirmed this incongruence. Our results highlight the metabolic diversity and variability within OTUs and add to the growing body of work suggesting 16S-based studies of Streptomyces fail to resolve important ecological and metabolic characteristics.

RevDate: 2019-10-16

Imchen M, Kumavath R, Vaz ABM, et al (2019)

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages.

Frontiers in microbiology, 10:2103.

Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.

RevDate: 2019-10-16

Fernández J, Ledesma E, Monte J, et al (2019)

Traditional Processed Meat Products Re-designed Towards Inulin-rich Functional Foods Reduce Polyps in Two Colorectal Cancer Animal Models.

Scientific reports, 9(1):14783 pii:10.1038/s41598-019-51437-w.

Inulin-rich foods exert a prebiotic effect, as this polysaccharide is able to enhance beneficial colon microbiota populations, giving rise to the in situ production of short-chain fatty acids (SCFAs) such as propionic and butyric acids. These SCFAs are potent preventive agents against colorectal cancer due to their histone deacetylases inhibitory properties, which induce apoptosis in tumor colonocytes. As colorectal cancer is the fourth most common neoplasia in Europe with 28.2 new cases per 100,000 inhabitants, a cost-effective preventive strategy has been tested in this work by redesigning common porcine meat products (chorizo sausages and cooked ham) consumed by a substantial proportion of the population towards potential colorectal cancer preventive functional foods. In order to test the preventive effect of these inulin-rich meat products against colorectal cancer, an animal model (Rattus norvegicus F344) was used, involving two doses of azoxymethane (10 mg/kg) and two treatments with dextran sodium sulfate (DSS) during a 20-week assay period. Control feed, control sausages, functional sausages (15.7% inulin), control cooked ham and functional cooked ham (10% inulin) were used to feed the corresponding animal cohorts. Then, the animals were sacrificed and their digestive tract tissues were analyzed. The results showed a statistically significant 49% reduction in the number of colon polyps in the functional meat products cohorts with respect to the control meat products animals, as well as an increase in the cecum weight (an indicator of a diet rich in prebiotic fiber), a 51.8% increase in colon propionate production, a 39.1% increase in colon butyrate concentrations, and a reduction in the number of hyperplastic Peyer's patches. Metagenomics studies also demonstrated colon microbiota differences, revealing a significant increase in Bacteroidetes populations in the functional meat products (mainly due to an increase in Bacteroidaceae and Prevotellaceae families, which include prominent propionate producers), together with a reduction in Firmicutes (especially due to lower Lachnospiraceae populations). However, functional meat products showed a remarkable increase in the anti-inflammatory and fiber-fermentative Blautia genus, which belongs to this Lachnospiraceae family. The functional meat products cohorts also presented a reduction in important pro-inflammatory bacterial populations, such as those of the genus Desulfovibrio and Bilophila. These results were corroborated in a genetic animal model of CRC (F344/NSlc-Apc1588/kyo) that produced similar results. Therefore, processed meat products can be redesigned towards functional prebiotic foods of interest as a cost-effective dietary strategy for preventing colorectal cancer in human populations.

RevDate: 2019-10-16

Woolhouse M, Ashworth J, Bogaardt C, et al (2019)

Sample descriptors linked to metagenomic sequencing data from human and animal enteric samples from Vietnam.

Scientific data, 6(1):202 pii:10.1038/s41597-019-0215-2.

There is still limited information on the diversity of viruses co-circulating in humans and animals. Here, we report data obtained from a large field collection of enteric samples taken from humans, pigs, rodents and other mammal hosts in Vietnam between 2012 and 2016. Each of 2100 stool or rectal swab samples was subjected to virally-enriched agnostic metagenomic sequencing; the short read sequence data are accessible from the European Nucleotide Archive (ENA). We link the sequence data to metadata on host type and demography and geographic location, distinguishing hospital patients, members of a cohort identified as a high risk of zoonotic infections (e.g. abattoir workers, rat traders) and animals. These data are suitable for further studies of virus diversity and virus discovery in humans and animals from Vietnam and to identify viruses found in multiple hosts that are potentially zoonotic.

RevDate: 2019-10-16

Agarwal N, Narnoliya LK, SP Singh (2019)

Characterization of a novel amylosucrase gene from the metagenome of a thermal aquatic habitat, and its use in turanose production from sucrose biomass.

Enzyme and microbial technology, 131:109372.

Turanose is a natural isomer of sucrose. It is an emerging functional sweetener of the next generation. Turanose is catalytically synthesized from the sucrose biomass by employing amylosucrase enzyme. In this study, a novel gene encoding amylosucrase (Asmet) has been identified from the metagenome of a thermal aquatic habitat. Asmet exhibits 37-55% identity at the protein level with the known amylosucrases characterized till date. Asmet was cloned and expressed in Escherichia coli, followed by protein purification, and characterization. Asmet protein exhibited the maximum total activity at 9.0 pH and 60 °C temperature, whereas, 8.0 pH and 50 °C temperature were found optimum for transglycosylation activity. Asmet showed fairly high thermal tolerance at 50 °C. The conjugation of Asmet protein with functionalized iron nanoparticles significantly improved its thermal tolerance, showing hardly any loss in the enzyme's activity even after 72 h of heat (50 °C) exposure. The turanose yield of about 47% was achieved from 1.5 M sucrose, containing 0.5 M fructose in the reaction. Turanose was purified (˜95%) via a bio-physical process, and characterized by TLC, HPLC, and NMR. The novel amylosucrase gene was demonstrated to be a potential candidate for turanose production, utilizing various sucrose containing feedstocks.

RevDate: 2019-10-16

Altan E, Li Y, Sabino-Santos G, et al (2019)

Viruses in Horses with Neurologic and Respiratory Diseases.

Viruses, 11(10): pii:v11100942.

Metagenomics was used to identify viral sequences in the plasma and CSF (cerobrospinal fluid) of 13 horses with unexplained neurological signs and in the plasma and respiratory swabs of 14 horses with unexplained respiratory signs. Equine hepacivirus and two copiparvoviruses (horse parvovirus-CSF and a novel parvovirus) were detected in plasma from neurological cases. Plasma from horses with respiratory signs contained the same two copiparvoviruses plus equine pegivirus D and respiratory swabs contained equine herpes virus 2 and 5. Based on genetic distances the novel copiparvovirus qualified as a member of a new parvovirus species we named Eqcopivirus. These samples plus another 41 plasma samples from healthy horses were tested by real-time PCRs for multiple equine parvoviruses and hepacivirus. Over half the samples tested were positive for one to three viruses with eqcopivirus DNA detected in 20.5%, equine hepacivirus RNA and equine parvovirus-H DNA in 16% each, and horse parvovirus-CSF DNA in 12% of horses. Comparing viral prevalence in plasma none of the now three genetically characterized equine parvoviruses (all in the copiparvovirus genus) was significantly associated with neurological and respiratory signs in this limited sampling.

RevDate: 2019-10-16

Gu J, Mao B, Cui S, et al (2019)

Metagenomic Insights into the Effects of Fructooligosaccharides (FOS) on the Composition of Luminal and Mucosal Microbiota in C57BL/6J Mice, Especially the Bifidobacterium Composition.

Nutrients, 11(10): pii:nu11102431.

Fructooligosaccharides (FOS) are considered prebiotics and have been proven to selectively promote the growth of Bifidobacterium in the gut. This study aimed to clarify the effects of FOS intake on the composition of luminal and mucosal microbiota in mice. Briefly, mice were fed a 0% or 25% FOS (w/w)-supplemented diet for four weeks, and the composition of luminal and mucosal microbiota, especially the Bifidobacterium, was analyzed by sequencing the V3-V4 region of 16S rRNA and groEL gene, respectively. After FOS intervention, there were significant increases in the total and wall weights of the cecum and the amount of total short-chain fatty acids (SCFAs) in the cecal contents of the mice. At the phylum level, the results showed a significant increase in the relative abundance of Actinobacteria in the contents and mucosa from the cecum to the distal colon in the FOS group. Besides Bifidobacterium, a significant increase was observed in the relative abundance of Coprococcus in all samples at the genus level, which may be partially related to the increase in butyric acid levels in the luminal contents. Furthermore, groEL sequencing revealed that Bifidobacterium pseudolongum was almost the sole bifidobacterial species in the luminal contents (>98%) and mucosa (>89%). These results indicated that FOS can selectively promote B. pseudolongum proliferation in the intestine, either in the lumen or the mucosa from the cecum to the distal colon. Further studies are required to reveal the competitive advantage of B. pseudolongum over other FOS-metabolizing bacteria and the response mechanisms of B. pseudolongum to FOS.

RevDate: 2019-10-16

Tu J, Chen L, Gao S, et al (2019)

Obtaining Genome Sequences of Mutualistic Bacteria in Single Microcystis Colonies.

International journal of molecular sciences, 20(20): pii:ijms20205047.

Cells of Microcystis are associated with heterotrophic bacteria and organized in colonies in natural environment, which are basic elements in the mass occurrence of cyanobacterial species. Analyzing these colonies by using metagenomics is helpful to understand species composition and relationship. Meanwhile, the difference in population abundance among Microcystis colonies could be used to recover genome bins from metagenome assemblies. Herein, we designed a pipeline to obtain high-quality genomes of mutualistic bacteria from single natural Microcystis colonies. Single colonies were lysed, and then amplified by using multiple displacement amplification to overcome the DNA quantity limit. A two-step assembly was performed after sequencing and scaffolds were grouped into putative bins based on their differential-coverage among species. We analyzed six natural colonies of three prevailing Microcystis species from Lake Taihu. Clustering results proved that colonies of the same species were similar in the microbial community composition. Eight putative population genome bins with wide bacterial diversity and different GC content were identified based on coverage difference among colonies. At the phylum level, proteobacteria was the most abundant besides cyanobacteria. Six of the population bins were further refined into nearly complete genomes (completeness > 90%).

RevDate: 2019-10-16

Sapi E, Kasliwala RS, Ismail H, et al (2019)

The Long-Term Persistence of Borrelia burgdorferi Antigens and DNA in the Tissues of a Patient with Lyme Disease.

Antibiotics (Basel, Switzerland), 8(4): pii:antibiotics8040183.

Whether Borrelia burgdorferi, the causative agent of Lyme disease, can persist for long periods in the human body has been a controversial question. The objective of this study was to see if we could find B. burgdorferi in a Lyme disease patient after a long clinical course and after long-term antibiotic treatment. Therefore, we investigated the potential presence of B. burgdorferi antigens and DNA in human autopsy tissues from a well-documented serum-, PCR-, and culture-positive Lyme disease patient, a 53-year-old female from northern Westchester County in the lower Hudson Valley Region of New York State, who had received extensive antibiotic treatments during extensive antibiotic treatments over the course of her 16-year-long illness. We also asked what form the organism might take, with special interest in the recently found antibiotic-resistant aggregate form, biofilm. We also examined the host tissues for the presence of inflammatory markers such as CD3+ T lymphocytes. Autopsy tissue sections of the brain, heart, kidney, and liver were analyzed by histological and immunohistochemical methods (IHC), confocal microscopy, fluorescent in situ hybridization (FISH), polymerase chain reaction (PCR), and whole-genome sequencing (WGS)/metagenomics. We found significant pathological changes, including borrelial spirochetal clusters, in all of the organs using IHC combined with confocal microscopy. The aggregates contained a well-established biofilm marker, alginate, on their surfaces, suggesting they are true biofilm. We found B. burgdorferi DNA by FISH, polymerase chain reaction (PCR), and an independent verification by WGS/metagenomics, which resulted in the detection of B. burgdorferi sensu stricto specific DNA sequences. IHC analyses showed significant numbers of infiltrating CD3+ T lymphocytes present next to B. burgdorferi biofilms. In summary, we provide several lines of evidence that suggest that B. burgdorferi can persist in the human body, not only in the spirochetal but also in the antibiotic-resistant biofilm form, even after long-term antibiotic treatment. The presence of infiltrating lymphocytes in the vicinity of B. burgdorferi biofilms suggests that the organism in biofilm form might trigger chronic inflammation.

RevDate: 2019-10-16

Ambrosino L, Tangherlini M, Colantuono C, et al (2019)

Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives.

Marine drugs, 17(10): pii:md17100576.

The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.

RevDate: 2019-10-16
CmpDate: 2019-10-16

Li Y, Guo Y, Wen Z, et al (2018)

Weaning Stress Perturbs Gut Microbiome and Its Metabolic Profile in Piglets.

Scientific reports, 8(1):18068 pii:10.1038/s41598-018-33649-8.

Weaned piglets are vulnerable to nutritional, physiological, and psychological stressors, leading to abrupt taxonomic and functional shifts in the intestinal microbiome. In this study, an integrated approach combination of 16S rDNA gene sequencing and the mass spectrometry-based metabolomics techniques was used to investigate the effects of weaning stress on intestinal microbial composition and its metabolic profiles of piglets. Three litters of suckling piglets with same parity were chosen. The samples of colonic contents were collected from each selected piglets (weaned day, 3 days after weaned) for microbial and metabolomics analysis. The results showed that Lachnospiraceae, Negativicutes, Selenomonadales, Campylobacterales and other 15 species increased after weaning, while Porphyromonadaceace, Alloprevotella, Barnesiella and Oscillibacter decreased. Based on the function profiles prediction and metabolomic analysis, five key metabolic pathways including Phenylalanine metabolism, Citrate cycle (TCA cycle), Glycolysis or Gluconeogenesis, Propanoate metabolism, Nicotinate and nicotinamide metabolism might be the relevant pathways involved in weaning stress-induced gut microbiota dysbiosis. Taken together, these results indicated that weaning stress not only changed microbial composition and function but altered the microbial metabolic profiles in the intestine, which might provide a new insight in alleviating weaning stress and facilitating disease prevention during the period of weaning in piglets.

RevDate: 2019-10-16
CmpDate: 2019-10-16

Piredda R, Claverie JM, Decelle J, et al (2018)

Diatom diversity through HTS-metabarcoding in coastal European seas.

Scientific reports, 8(1):18059 pii:10.1038/s41598-018-36345-9.

Diatoms constitute a diverse lineage of unicellular organisms abundant and ecologically important in aquatic ecosystems. Compared to other protists, their biology and taxonomy are well-studied, offering the opportunity to combine traditional approaches and new technologies. We examined a dataset of diatom 18S rRNA- and rDNA- (V4 region) reads from different plankton size-fractions and sediments from six European coastal marine sites, with the aim of identifying peculiarities and commonalities with respect to the whole protistan community. Almost all metabarcodes (99.6%) were assigned to known genera (121) and species (236), the most abundant of which were those already known from classic studies and coincided with those seen in light microscopy. rDNA and rRNA showed comparable patterns for the dominant taxa, but rRNA revealed a much higher diversity particularly in the sediment communities. Peculiar to diatoms is a tight bentho-pelagic coupling, with many benthic or planktonic species colonizing both water column and sediments and the dominance of planktonic species in both habitats. Overall metabarcoding results reflected the marked specificity of diatoms compared to other protistan groups in terms of morphological and ecological characteristics, at the same time confirming their great potential in the description of protist communities.

RevDate: 2019-10-16
CmpDate: 2019-10-16

Beyter D, Lin MS, Yu Y, et al (2018)

ProteoStorm: An Ultrafast Metaproteomics Database Search Framework.

Cell systems, 7(4):463-467.e6.

Shotgun metaproteomics has the potential to reveal the functional landscape of microbial communities but lacks appropriate methods for complex samples with unknown compositions. In the absence of prior taxonomic information, tandem mass spectra would be searched against large pan-microbial databases, which requires heavy computational workload and reduces sensitivity. We present ProteoStorm, an efficient database search framework for large-scale metaproteomics studies, which identifies high-confidence peptide-spectrum matches (PSMs) while achieving a two-to-three orders-of-magnitude speedup over popular tools. A reanalysis of a urinary tract infection (UTI) dataset of 110 individuals revealed a complex pattern of polymicrobial expression, including sub-types of UTIs, cases of bacterial vaginosis, and evidence of no underlying disease. Importantly, compared to the initial UTI study that restricted the search database to a manually curated list of 20 genera, ProteoStorm identified additional genera that were previously unreported, including a case of infection with the rare pathogen Propionimicrobium.

RevDate: 2019-10-16
CmpDate: 2019-10-16

Richardson JB, Dancy BCR, Horton CL, et al (2018)

Exposure to toxic metals triggers unique responses from the rat gut microbiota.

Scientific reports, 8(1):6578.

Our understanding of the interaction between the gut microbiota and host health has recently improved dramatically. However, the effects of toxic metal exposure on the gut microbiota remain poorly characterized. As this microbiota creates a critical interface between the external environment and the host's cells, it may play an important role in host outcomes during exposure. We therefore used 16S ribosomal RNA (rRNA) gene sequencing to track changes in the gut microbiota composition of rats exposed to heavy metals. Rats were exposed daily for five days to arsenic, cadmium, cobalt, chromium, nickel, or a vehicle control. Significant changes to microbiota composition were observed in response to high doses of chromium and cobalt, and significant dose-dependent changes were observed in response to arsenic, cadmium and nickel. Many of these perturbations were not uniform across metals. However, bacteria with higher numbers of iron-importing gene orthologs were overly represented after exposure to arsenic and nickel, suggesting some possibility of a shared response. These findings support the utility of the microbiota as a pre-clinical tool for identifying exposures to specific heavy metals. It is also clear that characterizing changes to the functional capabilities of microbiota is critical to understanding responses to metal exposure.

RevDate: 2019-10-15

Liang J, Mao G, Yin X, et al (2019)

Identification and quantification of bacterial genomes carrying antibiotic resistance genes and virulence factor genes for aquatic microbiological risk assessment.

Water research, 168:115160 pii:S0043-1354(19)30934-0 [Epub ahead of print].

Aquatic ecosystems have been increasingly threatened by anthropogenic activities, e.g., wastewater discharge and farm operation. Several methods are adopted to evaluate the effects of anthropogenic activities on biological risk in the environment, such as qPCR and amplicon next-generation sequencing. However, these methods fall short of providing genomic information of target species, which is vital for risk assessment from genomic aspect. Here, we developed a novel approach integrating metagenomic analysis and flow cytometry to identify and quantify potential pathogenic antibiotic resistant bacteria (PARB; carrying both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs)) in the environment, which are of particular concern due to their infection ability and antibiotic resistance. Based on the abundance/density of PARB, we evaluated microbiological risk in a river impacted by both municipal drainage and agriculture runoff. We collected samples upstream (mountainous area) as the control. Results showed that 81.8% of dominant PARB (33) recovered using our approach were related to known pathogenic taxa. In addition, intragenomic ARGs-VFGs coexistence patterns in the dominant Pseudomonas genomes (20 out of 71 PARB) showed high similarity with the most closely related Pseudomonas genomes from the NCBI RefSeq database. These results reflect acceptable reliability of the approach for (potential) pathogen identification in environmental samples. According to the PARB density, microbiological risk in samples from the agricultural area was significantly higher than in samples from the urban area. We speculated that this was due to the higher antibiotic usage in agriculture as well as intragenomic ARGs-VFGs co-evolution under antibiotic selective pressure. This study provides an alternative approach for the identification and quantification of PARB in aquatic environments, which can be applied for microbiological risk assessment.

RevDate: 2019-10-15

Sukumar S, Martin FE, Hughes TE, et al (2019)

Think Before you Prescribe: How Dentistry Contributes to Antibiotic Resistance.

Australian dental journal [Epub ahead of print].

Antibiotic resistance presents a daunting challenge to health professionals world-wide and has the potential to create major problems for modern healthcare, resulting in more medical expenditure, extended hospital stays and increased morbidity and mortality. Advanced genome sequencing technologies present a complex picture of resistance, extending our understanding beyond the pharmacotherapeutic interface between pathogens and antibiotics. This review discusses the global scope and scale of antibiotic resistance and contextualises it for the dental practitioner, emphasising the role we must play in limiting the progression of resistance through antibiotic stewardship and disease prevention.

RevDate: 2019-10-15

Andersen S, Staudacher H, Weber N, et al (2019)

Pilot study investigating the effect of enteral and parenteral nutrition on the gastrointestinal microbiome post-allogeneic transplantation.

British journal of haematology [Epub ahead of print].

Nutrition support is frequently required post-allogeneic haematopoietic progenitor cell transplantation (HPCT); however, the impact of mode of feeding on the gastrointestinal microbiome has not been explored. This study aimed to determine if there is a difference in the microbiome between patients receiving enteral nutrition (EN) and parenteral nutrition (PN) post-allogeneic HPCT. Twenty-three patients received either early EN or PN when required. Stool samples were collected at 30 days post-transplant and analysed with shotgun metagenomic sequencing. There was no difference in microbial diversity between patients who received predominantly EN (n = 13) vs. PN (n = 10) however patients who received predominantly EN had greater abundance of Faecalibacterium (P < 0·001) and ruminococcus E bromii (P = 0·026). Patients who had minimal oral intake for a longer duration during provision of nutrition support had a different overall microbial profile (P = 0·044), lower microbial diversity (P = 0·004) and lower abundance of faecalibacterium prausnitzii_C (P = 0·030) and Blautia (P = 0·007) compared to patients with greater oral intake. Lower microbial diversity was found in patients who received additional beta lactam antibiotics (P = 0·042) or had a longer length of hospital stay (P = 0·019). Post-HPCT oral intake should be encouraged to maintain microbiota diversity and, if nutrition support is required, EN may promote a more optimal microbiota profile.

RevDate: 2019-10-15

Rattes de Almeida Couto C, Catharine de Assis Leite D, Jurelevicius D, et al (2019)

Chemical and biological dispersants differently affect the bacterial communities of uncontaminated and oil-contaminated marine water.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] pii:10.1007/s42770-019-00153-8 [Epub ahead of print].

The use of dispersants in marine environments is a common practice worldwide for oil spill remediation. While the effects of chemical dispersants have been extensively studied, those of biosurfactants, mainly surfactin that is considered one of the most effective surfactants produced by bacteria, have been less considered. We constructed microcosms containing marine water collected from Grumari beach (W_GB, Brazil) and from Schiermonnikoog beach (W_SI, The Netherlands) with the addition of oil (WO), Ultrasperse II plus oil (WOS), surfactin plus oil (WOB), and both dispersants (WS or WB) individually. In these treatments, the composition of bacterial communities and their predictive biodegradation potential were determined over time. High-throughput sequencing of the rrs gene encoding bacterial 16S rRNA revealed that Bacteroidetes (Flavobacteria class) and Proteobacteria (mainly Gammaproteobacteria and Alphaproteobacteria classes) were the most abundant phyla found among the W_GB and W_SI microbiomes, and the relative abundance of the bacterial types in the different microcosms varied based on the treatment applied. Non-metrical multidimensional scaling (NMDS) revealed a clear clustering based on the addition of oil and on the dispersant type added to the GB or SI microcosms, i.e., WB and WOB were separated from WS and WOS in both marine ecosystems studied. The potential presence of diverse enzymes involved in oil degradation was indicated by predictive bacterial metagenome reconstruction. The abundance of predicted genes for degradation of petroleum hydrocarbons increased more in surfactin-treated microcosms than those treated with Ultrasperse II, mainly in the marine water samples from Grumari beach.

RevDate: 2019-10-15

Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, et al (2019)

Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity.

The Journal of infectious diseases pii:5586940 [Epub ahead of print].

Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.

RevDate: 2019-10-15

Araos R, Battaglia T, Ugalde JA, et al (2019)

Fecal Microbiome Characteristics and the Resistome Associated With Acquisition of Multidrug-Resistant Organisms Among Elderly Subjects.

Frontiers in microbiology, 10:2260.

Infections caused by multidrug-resistant organisms (MDRO) lead to considerable morbidity and mortality. The elderly population residing in nursing homes are a major reservoir of MDRO. Our objective was to characterize the fecal microbiome of 82 elderly subjects from 23 nursing homes and compare their resistome to that of healthy young persons. Comparisons of microbiome composition and the resistome between subjects who acquired MDRO or not were analyzed to characterize specific microbiome disruption indices (MDI) associated with MDRO acquisition. An approach based on both 16S rRNA amplicon and whole metagenome shotgun (WMS) sequencing data was used. The microbiome of the study cohort was substantially perturbed, with Bacteroides, Firmicutes, and Proteobacteria predominating. Compared to healthy persons, the cohort of elderly persons had an increased number, abundance, and diversity of antimicrobial resistance genes. High proportions of study subjects harbored genes for multidrug-efflux pumps (96%) and linezolid resistance (52%). Among the 302 antimicrobial resistance gene families identified in any subject, 60% were exclusively detected within the study cohort, including Class D beta-lactamase genes. Subjects who acquired MDRO or not had significant differences in bacterial taxa; Odoribacter laneus, and Akkermansia muciniphila were significantly greater among subjects who did not acquire MDRO whereas Blautia hydrogenotrophica predominated among subjects who acquired MDRO. These findings suggest that specific MDI may identify persons at high risk of acquiring MDRO.

RevDate: 2019-10-15

Hoarfrost A, Nayfach S, Ladau J, et al (2019)

Global ecotypes in the ubiquitous marine clade SAR86.

The ISME journal pii:10.1038/s41396-019-0516-7 [Epub ahead of print].

SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by the strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world's oceans, creating global maps of SAR86 ecotype distributions. Our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades.

RevDate: 2019-10-15

Nagata N, Tohya M, Takeuchi F, et al (2019)

Effects of storage temperature, storage time, and Cary-Blair transport medium on the stability of the gut microbiota.

Drug discoveries & therapeutics [Epub ahead of print].

How long fecal samples can withstand a period of refrigeration or room temperature, and the appropriate preservative, are largely unknown. Cary-Blair transport medium has been used for many years because it is inexpensive and prevents bacterial overgrowth. However, its effectiveness for metagenomic analyses has never been tested. We found that the microbial compositions using a 16S rRNA sequence of samples left at 4°C for 3 or 7 days or at 25°C for 1, 3, or 7 days differed significantly from samples stored at -80°C in no-preservative method. Whereas samples stored in Cary-Blair medium remained unchanged for longer periods. The relative abundances of phylum Bacteroidetes and Actinobacteria, changed significantly at 25°C, whereas Cary-Blair medium inhibited the reduction in Bacteroidetes and the increase in Actinobacteria. The bacterial survival counts were significantly lower in the RNAlater samples than in the Cary-Blair samples under aerobic and anaerobic culture conditions. In conclusion, storage time and storage temperature significantly affect the gut microbial composition in fecal samples. Given the low cost, inhibitory effect on bacterial changes, and potential utility in bacterial isolation, Cary-Blair medium containers are suitable for large-scale or hospital-based microbiome studies, especially if direct freezing at -80°C is unavailable.

RevDate: 2019-10-15

Guitor AK, Raphenya AR, Klunk J, et al (2019)

Capturing the Resistome: A targeted capture method to reveal antibiotic resistance determinants in metagenomes.

Antimicrobial agents and chemotherapy pii:AAC.01324-19 [Epub ahead of print].

The identification and association of the nucleotide sequences encoding antibiotic resistance elements is critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, which are both heavily time-consuming operations. An accurate and sensitive method to identify both rare and common resistance elements in complex metagenomic samples is needed. Referencing the Comprehensive Antibiotic Resistance Database, we designed a set of 37,826 probes to specifically target over 2000 nucleotide sequences associated with antibiotic resistance in clinically relevant bacteria. Testing of this probeset on DNA libraries generated from multi-drug resistant bacteria to selectively capture resistance genes reproducibly produced higher reads on-target at greater length of coverage when compared to shotgun sequencing. We also identified additional resistance gene sequences from human gut microbiome samples that sequencing alone was not able to detect. Our method to capture the resistome enables sensitive gene detection in diverse environments where antibiotic resistance represents less than 0.1% of the metagenome.

RevDate: 2019-10-15

Yang X, Chen Y, Guo F, et al (2019)

Metagenomic analysis of the biotoxicity of titanium dioxide nanoparticles to microbial nitrogen transformation in constructed wetlands.

Journal of hazardous materials pii:S0304-3894(19)31330-5 [Epub ahead of print].

Extensive use of titanium dioxide nanoparticles (TiO2 NPs) in various products has increased the release of these particles into wastewater, posing potential environmental risks. As an ecological wastewater treatment facility, constructed wetland (CW) is an important sink of NPs. However, little is known about the effects of NPs on microbial nitrogen transformation and related genes in CWs. In this study, short-term (5 days) and long-term (60 days) exposure experiments were conducted to investigate the effect of TiO2 NPs (0, 1, and 50 mg/L) on microbial nitrogen removal in CWs. The results showed that nitrogen removal efficiency was decreased by 35%-51% after long-term exposure to TiO2 NPs. Metagenomic analysis further confirmed that TiO2 NPs declined the relative abundance of functional genes and those enzyme encoding genes involved in the nitrogen metabolism pathway and glycolysis metabolism process. Furthermore, our data proved that the indigent glycolysis metabolism process resulted in the shortage of electron (NADH) and energy sources (ATP), causing inefficient nitrogen removal. Overall, these results revealed that the accumulation of TiO2 NPs altered the genetic expression of biofilm in CWs, which had significant impacts on biological nitrogen transformation.

RevDate: 2019-10-15
CmpDate: 2019-10-15

Grey EK, Bernatchez L, Cassey P, et al (2018)

Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys.

Scientific reports, 8(1):8843.

Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer sets. While community dissimilarity patterns were consistent across primers and sampling effort, richness patterns were not, suggesting that richness estimates are extremely sensitive to primer choice and sampling effort. The survey detected 64 potential NIS, with COI identifying more known NIS from port checklists but 18 S identifying more operational taxonomic units shared between three or more ports that represent un-recorded potential NIS. Overall, we conclude that eDNA metabarcoding surveys can reveal global similarity patterns among ports across a broad array of taxa and can also detect potential NIS in these key habitats. However, richness estimates and species assignments require caution. Based on results of this study, we make several recommendations for port eDNA sampling design and suggest several areas for future research.

RevDate: 2019-10-15
CmpDate: 2019-10-15

Zhu Y, Zhang F, Zhang C, et al (2018)

Dynamic microbial succession of Shanxi aged vinegar and its correlation with flavor metabolites during different stages of acetic acid fermentation.

Scientific reports, 8(1):8612.

Shanxi aged vinegar (SAV), one of the famous Chinese vinegars, is produced by multispecies solid-state fermentation in which the acetic acid fermentation stage (AAF) is especially important. However, how bacterial succession and their metabolites change along with the different stages of AAF is still poorly understood. In this study, we investigated the dynamic bacterial succession and flavor formation in three batches of SAV using high-throughput sequencing and metabolomics approaches. It is interesting to find that AAF can be divided into three stages based on its bacterial community succession (early stage, days 0-4; medium stage, days 5-21; and later stage, days 22-26). Pantoea, Pediococcus, Lactococcus and Rhizobium played an important role in the early stage; Lactobacillus was dominant in the medium stage (67.72%); and Acetobacter, Komagataeibacter and Kroppenstedtia were the key bacteria in the later stage. A total of seven organic acids and 42 volatile constituents (esters, alcohol, ketones and aldehydes) were detected during the AAF. Spearman correlation analysis showed a significant correlation between the bacterial community and these flavor metabolites during the AAF of the SAV. This is the first report to explore the relationships between volatile flavor metabolites and bacterial community succession by a three-staged method and provide theoretical support for a flavor formation mechanism in traditional SAV.

RevDate: 2019-10-15
CmpDate: 2019-10-15

Jehrke L, Stewart FA, Droste A, et al (2018)

The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster.

Scientific reports, 8(1):6215.

The metabolic phenotype of an organism depends on a complex regulatory network, which integrates the plethora of intrinsic and external information and prioritizes the flow of nutrients accordingly. Given the rise of metabolic disorders including obesity, a detailed understanding of this regulatory network is in urgent need. Yet, our level of understanding is far from completeness and complicated by the discovery of additional layers in metabolic regulation, such as the impact of the microbial community present in the gut on the hosts' energy storage levels. Here, we investigate the interplay between genome variation, diet and the gut microbiome in the shaping of a metabolic phenotype. For this purpose, we reared a set of fully sequenced wild type Drosophila melanogaster flies under basal and nutritionally challenged conditions and performed metabolic and microbiome profiling experiments. Our results introduce the fly as a model system to investigate the impact of genome variation on the metabolic response to diet alterations and reveal candidate single nucleotide polymorphisms associated with different metabolic traits, as well as metabolite-metabolite and metabolite-microbe correlations. Intriguingly, the dietary changes affected the microbiome composition less than anticipated. These results challenge the current view of a rapidly changing microbiome in response to environmental fluctuations.

RevDate: 2019-10-14

Vickerman MM, JM Mansfield (2019)

Streptococcal peptides that signal Enterococcus faecalis cells carrying the pheromone-responsive conjugative plasmid pAM373.

Molecular oral microbiology [Epub ahead of print].

Pheromone-mediated conjugative transfer of enterococcal plasmids can contribute to the dissemination of genes involved in antibiotic resistance, fitness, and virulence among co-residents of mixed microbial communities. We have previously shown that intergeneric signaling by the Streptococcus gordonii strain Challis heptapeptide s.g.cAM373 (SVFILAA) induces an aggregation-substance-mediated mating response and facilitates plasmid transfer from Enterococcus faecalis cells carrying the pheromone-responsive plasmid pAM373 to both pheromone producing and non-pheromone producing oral streptococcal recipients. To further investigate the streptococcal pheromone-like peptides s.g.cAM373-like sequences were identified in the signal sequences of streptococcal CamG lipoproteins and their abilities to induce a mating response in E. faecalis/pAM373 cells were examined. Synthetic heptamers with the consensus sequence (A/S)-(I/V)-F-I-L-(A/V/T)-(S/A) induced AS-mediated clumping. The conserved pheromone ABC transporter encoded by S. gordonii genome loci SGO_RS02660 and SGO_RS02665 was identified and confirmed to be required for s.g.cAM373 activity. Functional assays of cultures supernatants from representative oral and blood isolates of S. gordonii showed that in addition to strains encoding s.g.cAM373, strain SK120, encoding the newly-identified pheromone s.g.cAM373-V (SVFILVA), was able to induce enterococcal clumping, whereas strains SK6, SK8, SK9 and SK86 which encoded s.g.cAM373-T (SVFILTA) did not elicit a detectable mating response. Absence of pheromone activity in supernatants of heterologous hosts encoding its CamG precursor suggested that s.g.cAM373-T was not effectively processed and/or transported. Overall, these studies demonstrated the distribution of active pheromone peptides among strains of S. gordonii, and support a potential role for enterococcal-streptococcal communication in contributing to genetic plasticity in the oral metagenome.

RevDate: 2019-10-14

Rodriguez C, Jary A, Hua C, et al (2019)

Pathogen identification by shotgun metagenomics of patients with necrotising soft-tissue infections.

The British journal of dermatology [Epub ahead of print].

BACKGROUND: Necrotising soft-tissue infections (NSTIs) are life-threatening, requiring broad-spectrum antibiotics. Their etiological diagnosis can be limited by poor performance of cultures and administration of antibiotics before surgery.

OBJECTIVES: We aimed to: (i) compare 16S-targeted metagenomics (TM) and unbiased semi-quantitative pan-microorganism DNA- and RNA-based shotgun metagenomics (SM) with cultures, (ii) identify patients who best benefit from metagenomics approaches, and (iii) detect the microbial pathogens in surrounding non-necrotic "healthy" tissues by SM metagenomics-based methods.

METHODS: A prospective observational study was performed to assess the analytic performance of standard cultures, TM, and SM on tissues from 34 patients with NSTIs. Pathogen identification obtained with these three methods were compared.

RESULTS: Thirty-four necrotic and 10 healthy tissues were collected from 34 patients. The performance of TM was inferior to that of the other methods (p<0.05), whereas SM performed better than standard culture, although the result was not statistically significant (p=0.08). SM was significantly more sensitive than TM for the detection of all bacteria (p=0.02) and standard culture for the detection of anaerobic bacteria (p<0.01). There was a strong correlation (r=0.71, Spearman correlation coefficient) between the semi-quantitative abundance of bacteria in the culture and the bacteria/human sequence ratio in SM. Low amounts of bacterial DNA were found in healthy tissues, suggesting a bacterial continuum between macroscopically "healthy" and necrotic tissue.

CONCLUSIONS: SM showed a significantly better ability to detect a broader range of pathogens than TM and identify strict anaerobes than standard culture. Diabetic patients with NSTIs appeared to benefit most from shotgun metagenomics. Finally, our results suggest a bacterial continuum between macroscopically "healthy" non-necrotic areas and necrotic tissues.

RevDate: 2019-10-14

Okazaki Y, Nishimura Y, Yoshida T, et al (2019)

Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake.

Environmental microbiology [Epub ahead of print].

Metagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and their ecological interaction with hosts remain poorly understood. Here, we conducted a metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion (<0.22 μm) and cellular (0.22-5.0 μm) fractions collected spatiotemporally from a deep freshwater lake (Lake Biwa, Japan). This simultaneously reconstructed 183 complete (i.e., circular) viral genomes and 57 bacterioplankton metagenome-assembled genomes. Analysis of metagenomic read coverage revealed vertical partitioning of the viral community analogous to the vertically stratified bacterioplankton community. The hypolimnetic community was generally stable during stratification, but occasionally shifted abruptly, presumably due to lysogenic induction. Genes involved in assimilatory sulfate reduction were encoded in 20 (10.9%) viral genomes, including those of dominant viruses, and may aid viral propagation in sulfur-limited freshwater systems. Hosts were predicted for 40 (21.9%) viral genomes, encompassing 10 phyla (or classes of Proteobacteria) including ubiquitous freshwater bacterioplankton lineages (e.g., Ca. Fonsibacter and Ca. Nitrosoarchaeum). Comparison with viral genomes derived from published metagenomes revealed viral phylogeographic connectivity in geographically isolated habitats. Notably, analogous to their hosts, actinobacterial viruses were among the most diverse, ubiquitous, and abundant viral groups in freshwater systems, with potential high lytic activity in surface waters. This article is protected by copyright. All rights reserved.

RevDate: 2019-10-14

Lin Y, Wang BX, Zhang NN, et al (2019)

Metagenomic Analysis Identified Stenotrophomonas maltophilia Pneumonia in an Infant Suffering From Unexplained Very Severe Pneumonia.

Frontiers in pediatrics, 7:380.

Pneumonia poses a significant global morbidity and mortality burden on children. Etiological diagnosis and matched anti-microbial therapy are particularly important for very severe pneumonia. Although great advances have been achieved in diagnostic approaches, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory bactiera in an UP case in infant. Stenotrophomonas maltophilia was the only bacterial pathogen detected in blood. Metagenomic sequencing also provided bacteria genomic sequences, which could be used to evaluate the role of this pathogen in the disease. This NGS method has the potential to improve the identification of causative organisms in patients with pneumonia and the delivery of appropriate, pathogen-directed antibiotic therapy.

RevDate: 2019-10-14

Shakya M, Lo CC, PSG Chain (2019)

Advances and Challenges in Metatranscriptomic Analysis.

Frontiers in genetics, 10:904.

Sequencing-based analyses of microbiomes have traditionally focused on addressing the question of community membership and profiling taxonomic abundance through amplicon sequencing of 16 rRNA genes. More recently, shotgun metagenomics, which involves the random sequencing of all genomic content of a microbiome, has dominated this arena due to advancements in sequencing technology throughput and capability to profile genes as well as microbiome membership. While these methods have revealed a great number of insights into a wide variety of microbiomes, both of these approaches only describe the presence of organisms or genes, and not whether they are active members of the microbiome. To obtain deeper insights into how a microbial community responds over time to their changing environmental conditions, microbiome scientists are beginning to employ large-scale metatranscriptomics approaches. Here, we present a comprehensive review on computational metatranscriptomics approaches to study microbial community transcriptomes. We review the major advancements in this burgeoning field, compare strengths and weaknesses to other microbiome analysis methods, list available tools and workflows, and describe use cases and limitations of this method. We envision that this field will continue to grow exponentially, as will the scope of projects (e.g. longitudinal studies of community transcriptional responses to perturbations over time) and the resulting data. This review will provide a list of options for computational analysis of these data and will highlight areas in need of development.

RevDate: 2019-10-14

Chiodi A, Comandatore F, Sassera D, et al (2019)

SeqDeχ: A Sequence Deconvolution Tool for Genome Separation of Endosymbionts From Mixed Sequencing Samples.

Frontiers in genetics, 10:853.

In recent years, the advent of NGS technology has made genome sequencing much cheaper than in the past; the high parallelization capability and the possibility to sequence more than one organism at once have opened the door to processing whole symbiotic consortia. However, this approach needs the development of specific bioinformatics tools able to analyze these data. In this work, we describe SeqDex, a tool that starts from a preliminary assembly obtained from sequencing a mixture of DNA from different organisms, to identify the contigs coming from one organism of interest. SeqDex is a fully automated machine learning-based tool exploiting partial taxonomic affiliations and compositional analysis to predict the taxonomic affiliations of contigs in an assembly. In literature, there are few methods able to deconvolve host-symbiont datasets, and most of them heavily rely on user curation and are therefore time consuming. The problem has strong similarities with metagenomic studies, where mixed samples are sequenced and the bioinformatics challenge is trying to separate contigs on the basis of their source organism; however, in symbiotic systems, additional information can be exploited to improve the output. To assess the ability of SeqDex to deconvolve host-symbiont datasets, we compared it to state-of-the-art methods for metagenomic binning and for host-symbiont deconvolution on three study cases. The results point out the good performances of the presented tool that, in addition to the ease of use and customization potential, make SeqDex a useful tool for rapid identification of endosymbiont sequences.

RevDate: 2019-10-14

Zhang B, Wu X, Tai X, et al (2019)

Variation in Actinobacterial Community Composition and Potential Function in Different Soil Ecosystems Belonging to the Arid Heihe River Basin of Northwest China.

Frontiers in microbiology, 10:2209.

Actinobacteria are known for their metabolic potential of producing diverse secondary metabolites such as antibiotics. Actinobacteria also playimportant roles in biogeochemical cycling and how soils develop. However, little is known about the effect of the vegetation type on the actinobacterial community structures in soils from arid regions. For these reasons, we have analyzed the actinobacterial communities of five types of ecosystem (tree grove, shrub, meadow, desert, and farm) in the Heihe river basin. Using 16S rRNA high-throughput sequencing, we found 11 classes of Actinobacteria, with dominant classes of Actinobacteria (36.2%), Thermoleophilia (28.3%), Acidimicrobiia (19.4%). Five classes, 15 orders, 20 families and 36 genera were present in all samples. The dominant generalist genera were Gaiella, Solirubrobacter, Nocardioides, Mycobacterium, and Pseudonocardia. The actinobacterial community structures were significantly affected by the environment and vegetation type. The diversity of the actinobacterial community in the desert ecosystem was high, and this ecosystem harbored the highest proportion of unclassified sequences, representing rare Actinobacteria. Functional metagenomic prediction, using PICRUSt, indicated that Actinobacteria play an important role in nitrogen cycling in both desert and cultivated farm ecosystems.

RevDate: 2019-10-14

Tett A, Huang KD, Asnicar F, et al (2019)

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.

Cell host & microbe pii:S1931-3128(19)30427-5 [Epub ahead of print].

Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.

RevDate: 2019-10-13

Janakiev T, Dimkić I, Bojić S, et al (2019)

Bacterial communities of plum phyllosphere and characterization of indigenous antagonistic Bacillus thuringiensis R3/3 isolate.

Journal of applied microbiology [Epub ahead of print].

AIMS: Characterization of bacterial communities diversity on four local plum cultivars in two phenological stages using culture-dependent and culture-independent methods and screening among culturable plum community for indigenous bacteria active against phytopathogens.

METHODS AND RESULTS: The bacterial communities associated with leaves and fruits of four local Serbian plum cultivars (Požegača, Ranka, Čačanska Lepotica and Čačanska Rodna) were investigated in two phenological stages during early (May) and late (July) fruit maturation. Metagenomic approach revealed Methylobacterium, Sphingomonas and Hymenobacter as dominant genera. The most frequently isolated representatives with cultivable approach were pseudomonads with P. syringae and P. graminis, most likely the resident species of plum community. Antagonistic Bacillus thuringiensis R3/3 isolate from plum phyllosphere had ability to produce exoenzymes, reduce the growth of phytopathogenic bacteria in co-culture environment and show quorum quenching activity.

CONCLUSIONS: Plum cultivar and growth season contribute to the structure of the bacterial community associated with plum. Plum phyllosphere is good source of antagonists effective against phytopathogens.

Knowledge of bacterial communities on plum will have an impact on studies related to phyllosphere ecology and biocontrol. Indigenous antagonistic isolate from plum B. thuringiensis R3/3 could be further investigated for potential use in biological control of plum diseases.

RevDate: 2019-10-13

Plewniak F, Koechler S, Le Paslier D, et al (2019)

In situ metabolic activities of uncultivated Ferrovum sp. CARN8 evidenced by metatranscriptomic analysis.

Research in microbiology pii:S0923-2508(19)30102-0 [Epub ahead of print].

Amongst iron-oxidizing bacteria playing a key role in the natural attenuation of arsenic in acid mine drainages (AMDs), members of the Ferrovum genus were identified in mine effluent or water treatment plants, and were shown to dominate biogenic precipitates in field pilot experiments. In order to address the question of the in situ activity of the uncultivated Ferrovum sp. CARN8 strain in the Carnoulès AMD, we assembled its genome using metagenomic and metatranscriptomic sequences and we determined standardized expression values for protein-encoding genes. Our results showed that this microorganism was indeed metabolically active and allowed us to sketch out its metabolic activity in its natural environment. Expression of genes related to the respiratory chain and carbon fixation suggests aerobic energy production coupled to ferrous iron oxidation and chemolithoautotrophic growth. Notwithstanding the presence of nitrogenase genes in its genome, expression data also indicated that Ferrovum sp. CARN8 relied on ammonium import rather than nitrogen fixation. The expression of flagellum and chemotaxis genes hints that at least a proportion of this strain population was motile. Finally, apart from some genes related to metal resistance showing surprisingly low expression values, genes involved in stress response were well expressed as expected in AMDs.

RevDate: 2019-10-14
CmpDate: 2019-10-14

Lin Z, Ye W, Zu X, et al (2018)

Integrative metabolic and microbial profiling on patients with Spleen-yang-deficiency syndrome.

Scientific reports, 8(1):6619.

Gut microbiota is recognized as an indispensable "metabolic organ" that plays crucial roles in maintaining human health or initiating diseases. Spleen-yang-deficiency syndrome (SYDS) is a common syndrome of Traditional Chinese Medicine (TCM) clinic. It is a complex phenotype reflecting the overall changes of metabolism which are mainly caused by digestive disorders. However, little is known about the changes of gut microbiota and metabolism in patients with SYDS, as well as the crosstalk between gut microbiota and host metabolism. In the current study, an integrative metabolic and microbial profiling was performed on plasma, urine and feces from recruited SYDS and healthy individuals by using a LC-QTOFMS-based metabolomic and 16 s rRNA sequencing approaches. Our results showed a potentially significant contribution of gut dysbiosis to the metabolic disorders in SYDS. By integrating the differential gut bacteria with the metabolites, the results revealed some active bacterium of norank_f_CFT112H7, f_lachnospiraceae and bacteroides were closely involved in host mucosal integrity, bile acid metabolism and polysaccharides decomposition. Therefore, our results indicated the probable involvement of gut microbiota in mediating the metabolic changes, which warrants a further investigation on the role of gut microbiota in modulating the pathogenesis of SYDS.

RevDate: 2019-10-12

Yang Y, Pan J, Zhou Z, et al (2019)

Complex microbial nitrogen-cycling networks in three distinct anammox-inoculated wastewater treatment systems.

Water research, 168:115142 pii:S0043-1354(19)30916-9 [Epub ahead of print].

Microbial nitrogen removal mediated by anaerobic ammonium oxidation (anammox) are cost-effective, yet it is time-consuming to accumulate the slow-growing anammox bacteria in conventional wastewater treatment plants (WWTPs). Inoculation of anammox enriched pellets is an effective way to establish anammox and achieve shortcut nitrogen removal in full-scale WWTPs. However, little is known about the complex microbial nitrogen-cycling networks in these anammox-inoculated WWTPs. Here, we applied metagenomic and metatranscriptomic tools to study the microbial nitrogen removal in three conventional WWTPs, which have been inoculated exogenous anammox pellets, representing partial-nitrification anammox (PNA) and nitrification-denitrification nitrogen removal processes. In the PNA system of Bali (BL), ammonia was partially oxidized by ammonia-oxidizing bacteria (AOB) Nitrosomonas and the oxidized nitrite and the remaining ammonium were directly converted to N2 by anammox bacteria Ca. Brocadia and Ca. Kuenenia. In the nitrification-denitrification system of Wenshan (WS), ammonia-oxidizing archaea (AOA) Thaumarchaeota unexpectedly dominated the nitrifying community in the presence of AOB Nitrosomonas. Meanwhile, the biomass yield of Ca. Brocadia was likely inhibited by the high biodegradable organic compound input and limited by substrate competitions from AOA, AOB, complete ammonia oxidizers (comammox) Nitrospira, nitrite-oxidizing bacteria (NOB) Nitrospira, and heterotrophic denitrifiers. Unexpectedly, comammox Nitrospira was the predominant nitrifier in the presence of AOB Nitrosomonas in the organic carbon-rich nitrification-denitrification system of Linkou (LK). These results clearly showed that distinct active groups were working in concert for an effective nitrogen removal in different WWTPs. This study confirmed the feasibility of anammox application in ammonium-rich systems by direct inoculation of the exogenous anammox pellets and improved our understanding of microbial nitrogen cycling in anammox-driven conventional WWTPs from both physiochemical and omics perspectives.

RevDate: 2019-10-12

Dubinsky V, Reshef L, Bar N, et al (2019)

Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.

Gastroenterology pii:S0016-5085(19)41416-9 [Epub ahead of print].

BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis.

METHODS: We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center in Israel. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent acute pouchitis (n=6), chronic pouchitis and Crohn's-like disease of the pouch (n=27), normal pouch from patient with ulcerative colitis (n=10), and normal pouch from patient with familial adenomatous polyposis (n=6). Fecal samples (n=234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by human intestinal epithelial cells HT-29.

RESULTS: Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics. However, 89% of those who completed a 4-weeks course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae but also beneficial species such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to non-related antibiotics including extended-spectrum beta-lactamases.

CONCLUSIONS: The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.

RevDate: 2019-10-12

Kayser BD, Prifti E, Lhomme M, et al (2019)

Elevated serum ceramides are linked with obesity-associated gut dysbiosis and impaired glucose metabolism.

Metabolomics : Official journal of the Metabolomic Society, 15(11):140 pii:10.1007/s11306-019-1596-0.

INTRODUCTION: Low gut microbiome richness is associated with dyslipidemia and insulin resistance, and ceramides and other sphingolipids are implicated in the development of diabetes.

OBJECTIVES: Determine whether circulating sphingolipids, particularly ceramides, are associated with alterations in the gut microbiome among obese patients with increased diabetes risk.

METHODS: This was a cross-sectional and longitudinal retrospective analysis of a dietary/weight loss intervention. Fasted serum was collected from 49 participants (41 women) and analyzed by HPLC-MS/MS to quantify 45 sphingolipids. Shotgun metagenomic sequencing of stool was performed to profile the gut microbiome.

RESULTS: Confirming the link to deteriorated glucose homeostasis, serum ceramides were positively correlated with fasting glucose, but inversely correlated with fasting and OGTT-derived measures of insulin sensitivity and β-cell function. Significant associations with gut dysbiosis were demonstrated, with SM and ceramides being inversely correlated with gene richness. Ceramides with fatty acid chain lengths of 20-24 carbons were the most associated with low richness. Diet-induced weight loss, which improved gene richness, decreased most sphingolipids. Thirty-one MGS, mostly corresponding to unidentified bacteria species, were inversely correlated with ceramides, including a number of Bifidobacterium and Methanobrevibacter smithii. Higher ceramide levels were also associated with increased metagenomic modules for lipopolysaccharide synthesis and flagellan synthesis, two pathogen-associated molecular patterns, and decreased enrichment of genes involved in methanogenesis and bile acid metabolism.

CONCLUSION: This study identifies an association between gut microbiota richness, ceramides, and diabetes risk in overweight/obese humans, and suggests that the gut microbiota may contribute to dysregulation of lipid metabolism in metabolic disorders.

RevDate: 2019-10-11

Li Q, Chen H, Zhang M, et al (2019)

Altered short chain fatty acid profiles induced by dietary fiber intervention regulate AMPK levels and intestinal homeostasis.

Food & function [Epub ahead of print].

The objective of this study was to investigate the effects of dietary intervention on intestinal microbiota-mediated change in short chain fatty acid (SCFA) profile and intestinal homeostasis. Sequencing of the 16S rDNA of gut bacteria, metagenomics, intestinal epithelial transcriptomics, and metabonomics were conducted. Results showed that the dietary interventions altered the microbiota composition of cecal digesta, microbiota-mediated metabolism, and the gene expression profile in intestinal epithelial cells. Compared with red meat-diet-fed mice, fiber-diet-fed mice presented a shift in the gut microbiome toward increased production of butanoate, which was accompanied by up-regulation of microbiota- and AMP-activated protein kinase (AMPK)-dependent gene expression and decrease in serum concentrations of trimethylamine N-oxide (TMAO), triglyceride (TG) and glucose (GLU). The results suggested a new regulatory mechanism via which butanoate and AMPK activation contributed to intestinal integrity and homeostasis by affecting metabolism, intestinal barrier function and transporter expression.

RevDate: 2019-10-11

Reddy KE, Kim HR, Jeong JY, et al (2019)

Impact of breed on the fecal microbiome of dogs under the same dietary condition.

Journal of microbiology and biotechnology pii:10.4014/jmb.1906.06048 [Epub ahead of print].

The gut microbiome influences the health and well-being of dogs. However, little is known about the impact of breed on the fecal microbiome composition in dogs. Therefore, we aimed to investigate the differences in the fecal microbiome in three breeds of dog fed and housed under the same conditions, namely eight Maltese (8.0 ± 0.1 years), eight Miniature Schnauzer (8.0 ± 0.0 years), and nine Poodle dogs (8.0 ± 0.0 years). Fresh fecal samples were collected from the dogs and used to extract metagenomic DNA. The composition of the fecal microbiome was evaluated by 16S rRNA gene amplicon sequencing on the MiSeq platform. A total of 840,501 sequences were obtained from the 25 fecal samples and classified as Firmicutes (32.3-97.3% of the total sequences), Bacteroidetes (0.1-62.6%), Actinobacteria (0.2-14.7%), Fusobacteria (0.0-5.7%), and Proteobacteria (0.0-5.1%). The relative abundance of Firmicutes was significantly lower in the Maltese dog breed than that in the other two breeds, while that of Fusobacteria was significantly higher in the Maltese than in the Miniature Schnauzer breed. At the genus level, the relative abundance of Streptococcus, Fusobacterium, Turicibacter, Succinivibrio, and Anaerobiospirillum differed significantly among the three dog breeds. These genera had no correlation with age, diet, sex, body weight, vaccination history, or parasite protection history. Within a breed, some of these genera had a correlation with at least one blood chemistry value. This study indicates that the composition of the fecal microbiome in dogs is affected by breed.

RevDate: 2019-10-10

Li Y, Tremblay J, Bainard LD, et al (2019)

Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production.

Environmental microbiology [Epub ahead of print].

Soil microorganisms play a critical role in the biosphere, and the influence of cropland fertilization on the evolution of soil as a living entity is being actively documented. In this study, we used a shotgun metagenomics approach to globally expose the effects of 50-year N and P fertilization of wheat on soil microbial community structure and function, and their potential involvement in overall N cycling. Nitrogen (N) fertilization increased alpha diversity in archaea and fungi while reducing it in bacteria. Beta diversity of archaea, bacteria, and fungi, as well as soil function, were also mainly driven by N fertilization. The abundance of archaea was negatively impacted by N fertilization while bacterial and fungal abundance was increased. The responses of N-metabolism-related genes to fertilization differed in archaea, bacteria, and fungi. All archaeal N metabolic processes were decreased by N fertilization, while denitrification, assimilatory nitrate reduction and organic-N metabolism were highly increased by N fertilization in bacteria. Nitrate assimilation was the main contribution of fungi to N cycling. Thaumarchaeota and Halobacteria in archaea; Actinobacteria, alpha-, beta-, gamma-, and delta Proteobacteria in bacteria; and Sordariomycetes in fungi participated dominantly and widely in soil N metabolic processes. This article is protected by copyright. All rights reserved.

RevDate: 2019-10-10

Martín-Cabello G, Terrón-González L, Ferrer M, et al (2019)

Identification of a complete dibenzothiophene biodesulfurization operon and its regulator by functional metagenomics.

Environmental microbiology [Epub ahead of print].

Functional screening for aromatic oxygenases ring of an oil contaminated soil metagenome identified 25 different clones bearing monooxygenases coding genes. One fosmid bore an operon containing 4 tightly linked genes coding for a complete dibenzothiophene biodesulfurization pathway, which included the predicted monooxygenases DszC and DszA, the desulfinase DszB, and an FMN-oxidoreductase designated DszE. The dszEABC operon provided E. coli with the ability to use dibenzothiophene as the only sulfur source. Transcription of the operon is driven from a σN -dependent promoter and regulated by an activator that was designated dszR. DszR has been purified and characterized in vitro, and shown to be a constitutively activeσN -dependent activator of the group IV, which binds to two contiguous sequences located upstream of the promoter. The dsz promoter, and dszE and dszR genes have apparently been recruited from an aliphatic sulfonate biodegradation pathway. If transcribed from a heterologous upstream promoter, the σN -dependent promoter region functions as an 'insulator' that prevents translation of dszE,, by binding with its ribosome binding site. Translational coupling, in turn, prevents translation of the downstream dszABC genes. The silencer combined with translational coupling thus represent an effective way of preventing expression of operons when spuriously transcribed from upstream promoters. This article is protected by copyright. All rights reserved.

RevDate: 2019-10-10

Zeng Y, Chen S, Fu Y, et al (2019)

Gut microbiota dysbiosis in patients with hepatitis B virus-induced chronic liver disease covering chronic hepatitis, liver cirrhosis and hepatocellular carcinoma.

Journal of viral hepatitis [Epub ahead of print].

The information regarding the effect of hepatitis B virus (HBV) infection on gut microbiota and the relationship between gut microbiota dysbiosis and hepatitis B virus-induced chronic liver disease (HBVCLD) is limited. In this study, we aimed at characterizing the gut microbiota composition in the three different stages of hepatitis B virus-induced chronic liver disease patients and healthy individuals. Fecal samples and clinical data were collected from HBVCLD patients and healthy individuals. The 16S rDNA gene amplification products were sequenced. Bioinformatic analysis including alpha-diversity, PICRUSt, etc. was performed. A total of 19 phyla, 43 classes, 72 orders, 126 families, and 225 genera were detected. The beta-diversity showed a separate clustering of healthy controls and HBVCLD patients covering chronic hepatitis (CHB), liver cirrhosis (LC), and hepatocellular carcinoma (HCC); and gut microbiota of healthy controls were more consistent, whereas those of CHB, LC and HCC varied substantially. The abundance of Firmicutes was lower, and Bacteroidetes was higher in patients with CHB, LC, and HCC than in healthy controls. Predicted metagenomics of microbial communities showed an increase in glycan biosynthesis and metabolism-related genes and lipid metabolism-related genes in HBVCLD than in healthy individuals. Our study suggested that HBVCLD is associated with gut dysbiosis, with characteristics including, a gain in potential bacteria and a loss in potential beneficial bacteria or genes. Further study of CHB, LC, and HCC based on microbiota may provide a novel insight into the pathogenesis of HBVCLD as well as a novel treatment strategy.

RevDate: 2019-10-10

Roshanzadeh A, Kang H, You SH, et al (2019)

Real-time monitoring of NADPH levels in living mammalian cells using fluorescence-enhancing protein bound to NADPHs.

Biosensors & bioelectronics, 146:111753 pii:S0956-5663(19)30832-2 [Epub ahead of print].

Nicotinamide adenine nucleotide phosphate (NADPH) has been known to be involved in the multiple pathways of cell metabolism. However, conventional quantification assays for NADPH have required breaking down the cell membranes of around one million cells per assay, and monitoring NADPH flux in living cells has been limited by a few available tools. Here, we visualized NADPH levels in human cervical cancer cells HeLa using metagenome-derived blue fluorescent protein (mBFP), which specifically binds to NADPH and enhances the intrinsic fluorescence of NADPH up to 10-fold when imaged by two-photon microscopy to reduce photodamage. Adding an oxidizing agent such as diamide to HeLa cells that expressed mBFP led to an immediate decrease of intracellular NADPH depending on glucose availability in culture media. Furthermore, inhibiting glucose-6-phosphate dehydrogenase (G6PD) in the pentose phosphate pathway with dehydroandrosterone (DHEA) and knockdown of G6PD transcripts gradually decreased NADPH when diamide was added to living cells. These results demonstrate that introducing a bacterial mBFP gene into mammalian cells is a straightforward approach to monitoring intracellular NADPH flux in real time at the single-cell level. Moreover, this strategy can be expanded to tracking the spatio-temporal changes in NADPH even in single-cell organelles such as mitochondria and chloroplasts, which will allow us to more precisely assess the efficacy of biochemically or biophysically metabolic perturbations in animal and plant cells.

RevDate: 2019-10-10

Shkoporov AN, Clooney AG, Sutton TDS, et al (2019)

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific.

Cell host & microbe, 26(4):527-541.e5.

The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterized, and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome. Using a database-independent approach that uses most of the sequencing data, we uncovered the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella, and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.

RevDate: 2019-10-10

Hendriksen RS, Lukjancenko O, Munk P, et al (2019)

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach.

PloS one, 14(10):e0222531 pii:PONE-D-19-16870.

BACKGROUND: Worldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate.

METHOD: We conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance.

RESULTS: A large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time.

CONCLUSION: The metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care.

RevDate: 2019-10-10

Tassoni L, Zamperin G, Schiavon E, et al (2019)

First whole genome characterization of porcine astrovirus detected in swine faeces in Italy.

Veterinaria italiana, 55(3):221-229.

Porcine astroviruses (PoAstV) are found in the gastrointestinal tract of healthy and diseased pigs worldwide. However, their role in causing enteric disease in pigs and other animals has not been elucidated. In the present report, we describe for the first time in Italy, the identification and genetic characterization, through whole genome sequencing, of a PoAstV2 in pigs in Northeast Italy in 2015. This instance is the first detection of PoAstV2 in pigs in Italy. The phylogenetic analysis of the complete ORF2 segment highlights the high similarity of this virus to those circulating that same year in Japan. There are very few full astrovirus genomes available, and the present data represent an important contribution towards a better understanding of the characteristics and evolution of these viruses.

RevDate: 2019-10-10

Shi N, Yang G, Wang P, et al (2019)

Complete genome sequence of a novel partitivirus from the entomogenous fungus Beauveria bassiana in China.

Archives of virology pii:10.1007/s00705-019-04428-1 [Epub ahead of print].

In this study, we report a novel double-stranded RNA (dsRNA) virus, Beauveria bassiana partitivirus 3 (BbPV-3), derived from the entomogenous fungus Beauveria bassiana isolate RCEF5853 from China. The genome of BbPV-3, whose sequence was determined by metagenomic sequencing, RT-PCR, and RACE cloning, comprises two dsRNA genome segments that are 1,856 and 1,719 bp long. The first segment contains a single ORF (ORF-1) encoding a 584-amino-acid-long protein (66.05 kDa) with a conserved RNA-dependent RNA polymerase (RdRp) motif. The second segment also has a single ORF (ORF-2) encoding a 500-amino-acid-long coat protein (CP) (55.9 kDa). The CP and RdRp sequences showed highest identity of 43.4% and 60.2%, respectively, to those of Colletotrichum eremochloae partitivirus 1. Phylogenetic analysis of the RdRp domain of the polyprotein revealed that BbPV-3 grouped together with the members of the genus Epsilonpartitivirus. Hence, we proposed that Beauveria bassiana partitivirus 3 is a novel member of the proposed genus Epsilonpartitivirus.

RevDate: 2019-10-10

Ma Y, Marais A, Lefebvre M, et al (2019)

Phytovirome Analysis of Wild Plant Populations: Comparison of Double-Stranded RNA and Virion-Associated Nucleic Acid Metagenomic Approaches.

Journal of virology pii:JVI.01462-19 [Epub ahead of print].

Metagenomic studies have indicated that the diversity of plant viruses was until recently far underestimated. As important components of ecosystems, there is a need to explore the diversity and richness of the viruses associated with plant populations and to understand the drivers shaping their diversity in space and time. Two viral sequence enrichment approaches, double-stranded RNA (dsRNA) and Virion-associated nucleic acids (VANA), have been used and compared here for the description of the virome of complex plant pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. A novel bioinformatics strategy was used to assess viral richness not only at family level but also by determining Operational Taxonomic Units (OTU) following the clustering of conserved viral domains. A large viral diversity, dominated by novel dsRNA viruses was detected in all sites while a large between sites variability limited the ability to draw clear conclusion on the impact of cultivation. A trend for a higher diversity of dsRNA viruses was nevertheless detected in unmanaged sites (118 vs 77 unique OTUs). The dsRNA-based approach consistently revealed a broader and more comprehensive diversity for RNA viruses than the VANA approach, whatever the assessment criterion. In addition, dissimilarity analyses indicated both approaches to be largely reproducible, but not necessarily convergent. These findings illustrate features of phytoviromes in various ecosystems and a novel strategy for precise virus richness estimation. These results allow to reason methodological choices in phytovirome studies and, likely in other viromes study where RNA viruses are the focal taxa.IMPORTANCE There are today significant knowledge gaps on phytovirus populations and on the drivers impacting them, but also on the comparative performance methodological approaches for their study. We used and compared two viral sequences enrichment approaches, double-stranded RNAs (dsRNA) and virion-associated nucleic acids (VANA) for phytovirome description in complex pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. Viral richness was assessed by determining Operational Taxonomic Units (OTU) following the clustering of conserved viral domains. There is some limited evidence of an impact of cultivation on viral populations. These results provide data allowing to reason the methodological choices in virome studies. For researchers primarily interested in RNA viruses, the dsRNA approach is advised because it consistently provided a more comprehensive description of the analysed phytoviromes, but it understandably underrepresented DNA viruses and bacteriophages.

RevDate: 2019-10-10

Peters BA, Wilson M, Moran U, et al (2019)

Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients.

Genome medicine, 11(1):61 pii:10.1186/s13073-019-0672-4.

BACKGROUND: Recent evidence suggests that immunotherapy efficacy in melanoma is modulated by gut microbiota. Few studies have examined this phenomenon in humans, and none have incorporated metatranscriptomics, important for determining expression of metagenomic functions in the microbial community.

METHODS: In melanoma patients undergoing immunotherapy, gut microbiome was characterized in pre-treatment stool using 16S rRNA gene and shotgun metagenome sequencing (n = 27). Transcriptional expression of metagenomic pathways was confirmed with metatranscriptome sequencing in a subset of 17. We examined associations of taxa and metagenomic pathways with progression-free survival (PFS) using 500 × 10-fold cross-validated elastic-net penalized Cox regression.

RESULTS: Higher microbial community richness was associated with longer PFS in 16S and shotgun data (p < 0.05). Clustering based on overall microbiome composition divided patients into three groups with differing PFS; the low-risk group had 99% lower risk of progression than the high-risk group at any time during follow-up (p = 0.002). Among the species selected in regression, abundance of Bacteroides ovatus, Bacteroides dorei, Bacteroides massiliensis, Ruminococcus gnavus, and Blautia producta were related to shorter PFS, and Faecalibacterium prausnitzii, Coprococcus eutactus, Prevotella stercorea, Streptococcus sanguinis, Streptococcus anginosus, and Lachnospiraceae bacterium 3 1 46FAA to longer PFS. Metagenomic functions related to PFS that had correlated metatranscriptomic expression included risk-associated pathways of L-rhamnose degradation, guanosine nucleotide biosynthesis, and B vitamin biosynthesis.

CONCLUSIONS: This work adds to the growing evidence that gut microbiota are related to immunotherapy outcomes, and identifies, for the first time, transcriptionally expressed metagenomic pathways related to PFS. Further research is warranted on microbial therapeutic targets to improve immunotherapy outcomes.

RevDate: 2019-10-10

Dreisbach C, Prescott S, J Alhusen (2019)

Influence of Maternal Prepregnancy Obesity and Excessive Gestational Weight Gain on Maternal and Child Gastrointestinal Microbiome Composition: A Systematic Review.

Biological research for nursing [Epub ahead of print].

BACKGROUND: Maternal obesity is a well-known risk factor for significant obstetric and neonatal complications. The influence of the gastrointestinal microbiome in the setting of maternal obesity during pregnancy is less understood. The purpose of this systematic review is to synthesize the literature on the relationships between maternal obesity and excessive gestational weight gain (EGWG) and the composition of maternal and child gastrointestinal microbiomes.

METHOD: We searched CINHAL, OVID Medline, Web of Science, and PubMed for relevant literature using medical subject heading terms related to obesity, pregnancy, and the gastrointestinal microbiome. We assessed 249 articles for potential inclusion using the preferred reporting items for systematic review and meta-analyses framework and deemed 11 articles as relevant for this review.

RESULTS: Maternal obesity was associated with significant microbial changes in both maternal and infant fecal microbiome biospecimens including increases in Bacteroidetes, Firmicutes, and the Actinobacteria phyla and decreases in Bifidobacteria. However, inconsistencies in uniform taxonomic results across all studies mean that evidence of specific microbial associations with obesity and EGWG is inconclusive.

CONCLUSION: Our findings suggest that both maternal and child gastrointestinal microbiome composition is altered in the setting of maternal obesity and EGWG during pregnancy. Future microbiome studies should concentrate on the investigation of metagenomic sequencing to elucidate microbial function rather than solely taxonomic composition. More diverse populations of mothers should be sampled to address health disparities and adverse outcomes of underrepresented populations. Finally, analytic pipelines should be standardized across studies to aid in reproducibility.

RevDate: 2019-10-10
CmpDate: 2019-10-09

Chatterjee A, K Kondabagil (2019)

Giant viral genomic signatures in the previously reported gut metagenomes of pre-school children in rural India.

Archives of virology, 164(11):2819-2822.

A recent study by Ghosh et al. compared the gut microbiomes of 20 preschool children from India and found an association between the gut microbiome and the nutritional status of the child. Here, we explored these metagenomes for the presence of genomic signatures of prokaryotic and eukaryotic viruses. Several of the viral signatures found in all 20 metagenomes belonged to giant viruses (GVs). In addition, we found hits for bacteriophages to several major human pathogens, including Shigella, Salmonella, Escherichia, and Enterobacter. Concurrently, we also detected several antibiotic resistance genes (ARGs) in the metagenomes. All of the ARGs detected in this study (beta-lactam, macrolide, metronidazole, and tetracycline) are associated with mobile genetic elements (MGEs) and have been reported to cause high levels of resistance to their respective antibiotics. Despite recent reports of giant viruses and their genomic signatures in gut microbiota, their role in human physiology remains poorly understood. The effect of cooccurrence of ARGs and GVs in the gut needs further investigation.

RevDate: 2019-10-10
CmpDate: 2019-10-09

Misic AM, Miedel EL, Brice AK, et al (2018)

Culture-independent Profiling of the Fecal Microbiome to Identify Microbial Species Associated with a Diarrheal Outbreak in Immunocompromised Mice.

Comparative medicine, 68(4):261-268.

Immunocompromised mice are used frequently in biomedical research, in part because they accommodate the engraftment and study of primary human cells within a mouse model; however, these animals are susceptible to opportunistic infections and require special husbandry considerations. In 2015, an outbreak marked by high morbidity but low mortality swept through a colony of immunocompromised mice; this outbreak rapidly affected 75% of the colony and ultimately required complete depopulation of the barrier suite. Conventional microbiologic and molecular diagnostics were unsuccessful in determining the cause; therefore, we explored culture-independent methods to broadly profile the microbial community in the feces of affected animals. This approach identified 4 bacterial taxa- Candidatus Arthromitus, Clostridium celatum, Clostridiales bacterium VE202-01, and Bifidobacterium pseudolongum strain PV8-2- that were significantly enriched in the affected mice. Based on these results, specific changes were made to the animal husbandry procedures for immunocompromised mice. This case report highlights the utility of culture-independent methods in laboratory animal diagnostics.

RevDate: 2019-10-10
CmpDate: 2019-10-10

Paul F, Otte J, Schmitt I, et al (2018)

Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens.

Scientific reports, 8(1):8624.

The implementation of HTS (high-throughput sequencing) approaches is rapidly changing our understanding of the lichen symbiosis, by uncovering high bacterial and fungal diversity, which is often host-specific. Recently, HTS methods revealed the presence of multiple photobionts inside a single thallus in several lichen species. This differs from Sanger technology, which typically yields a single, unambiguous algal sequence per individual. Here we compared HTS and Sanger methods for estimating the diversity of green algal symbionts within lichen thalli using 240 lichen individuals belonging to two species of lichen-forming fungi. According to HTS data, Sanger technology consistently yielded the most abundant photobiont sequence in the sample. However, if the second most abundant photobiont exceeded 30% of the total HTS reads in a sample, Sanger sequencing generally failed. Our results suggest that most lichen individuals in the two analyzed species, Lasallia hispanica and L. pustulata, indeed contain a single, predominant green algal photobiont. We conclude that Sanger sequencing is a valid approach to detect the dominant photobionts in lichen individuals and populations. We discuss which research areas in lichen ecology and evolution will continue to benefit from Sanger sequencing, and which areas will profit from HTS approaches to assessing symbiont diversity.

RevDate: 2019-10-10
CmpDate: 2019-10-09

ElNaker NA, Elektorowicz M, Naddeo V, et al (2018)

Assessment of Microbial Community Structure and Function in Serially Passaged Wastewater Electro-Bioreactor Sludge: An Approach to Enhance Sludge Settleability.

Scientific reports, 8(1):7013.

Several studies have been carried out to understand bulking phenomena and the importance of environmental factors on sludge settling characteristics. The main objective of this study was to carry out functional characterization of microbial community structure of wastewater electro-bioreactor sludge as it undergoes serial passaging in the presence or absence of a current density over 15 days. Illumina MiSeq sequencing and QIIME were used to assess sludge microbial community shifts over time. (α) and (β) diversity analysis were conducted to assess the microbial diversity in electro-bioreactors. A phylogeny-based weighted UniFrac distance analysis was used to compare between bacterial communities while BIO-ENV trend and Spearman's rank correlation analysis were performed to investigate how reactor operational parameters correlated with bacterial community diversity. Results showed that the removal efficiency of soluble chemical oxygen demand (sCOD) ranged from 91-97%, while phosphorous (PO43--P) removal was approximately 99%. Phylogenetic analysis revealed stark differences in the development of sludge microbial communities in the control and treatment reactor. There was no mention of any studies aimed at characterizing functional microbial communities under electric field and the results communicated here are the first, to our knowledge, that address this gap in the literature.

RevDate: 2019-10-10
CmpDate: 2019-10-09

Dittmer J, D Bouchon (2018)

Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare.

Scientific reports, 8(1):6998.

Wolbachia are widespread heritable endosymbionts of arthropods notorious for their profound effects on host fitness as well as for providing protection against viruses and eukaryotic parasites, indicating that they can interact with other microorganisms sharing the same host environment. Using the terrestrial isopod crustacean Armadillidium vulgare, its highly diverse microbiota (>200 bacterial genera) and its three feminizing Wolbachia strains (wVulC, wVulM, wVulP) as a model system, the present study demonstrates that Wolbachia can even influence the composition of a diverse bacterial community under both laboratory and natural conditions. While host origin is the major determinant of the taxonomic composition of the microbiota in A. vulgare, Wolbachia infection affected both the presence and, more importantly, the abundance of many bacterial taxa within each host population, possibly due to competitive interactions. Moreover, different Wolbachia strains had different impacts on microbiota composition. As such, infection with wVulC affected a higher number of taxa than infection with wVulM, possibly due to intrinsic differences in virulence and titer between these two strains. In conclusion, this study shows that heritable endosymbionts such as Wolbachia can act as biotic factors shaping the microbiota of arthropods, with as yet unknown consequences on host fitness.

RevDate: 2019-10-09

Berman HL, McLaren MR, BJ Callahan (2019)

Understanding and Interpreting Community Sequencing Measurements of the Vaginal Microbiome.

BJOG : an international journal of obstetrics and gynaecology [Epub ahead of print].

Community-wide high throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: 1) amplicon sequencing, 2) shotgun metagenomic sequencing, and 3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome.

RevDate: 2019-10-09

Kaufman JH, Elkins CA, Davis M, et al (2019)

Insular Microbiogeography: Three Pathogens as Exemplars.

Current issues in molecular biology, 36:89-108 pii:v36/89 [Epub ahead of print].

Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into question the long-held model of a hierarchical tree of life, which leads to questioning of the definition of a species. Large-scale studies of microbial genome diversity reveal that the cumulative number of new genes discovered increases with the number of genomes studied as a power law and subsequently leads to the lack of evidence for a unique core genome within closely related organisms. Sampling 'enough' new genomes leads to the discovery of a replacement or alternative to any gene. This power law behaviour points to an underlying self-organizing critical process that may be guided by mutation and niche selection. Microbes in any particular niche exist within a local web of organism interdependence known as the microbiome. The same mechanism that underpins the macro-ecological scaling first observed by MacArthur and Wilson also applies to microbial communities. Recent metagenomic studies of a food microbiome demonstrate the diverse distribution of community members, but also genotypes for a single species within a more complex community. Collectively, these results suggest that traditional taxonomic classification of bacteria could be replaced with a quasispecies model. This model is commonly accepted in virology and better describes the diversity and dynamic exchange of genes that also hold true for bacteria. This model will enable microbiologists to conduct population-scale studies to describe microbial behaviour, as opposed to a single isolate as a representative.

RevDate: 2019-10-09

Strazzulli A, Cobucci-Ponzano B, Iacono R, et al (2019)

Discovery of hyperstable carbohydrate-active enzymes through metagenomics of extreme environments.

The FEBS journal [Epub ahead of print].

The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy) to discover hyperthermophilic carbohydrate-active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T=85°C and pH 5.5; T=92°C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in-silico analysis led to 14,934 and 17,652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarcheaota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β-mannanase/β-1,3-glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD+ dependent GH109 with a previously unreported β-N-acetylglucosaminide/β-glucoside specificity.

RevDate: 2019-10-09

Hua ZS, Wang YL, Evans PN, et al (2019)

Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea.

Nature communications, 10(1):4574 pii:10.1038/s41467-019-12574-y.

Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.

RevDate: 2019-10-09

Sakowski E, Uritskiy G, Cooper R, et al (2019)

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.

mSystems, 4(5): pii:4/5/e00392-19.

Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses. We summarize the ideas generated by participants of the Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from the presentations that most fields have advanced beyond simple associative and descriptive analyses, most fields lack essential elements needed for the development and application of accurate microbiome predictions. Participants stressed the need for standardization, reproducibility, and accessibility of quantitative tools as key to advancing predictions in microbiome analysis. We highlight hurdles that participants identified and propose directions for future efforts that will advance the use of prediction in microbiome research.

RevDate: 2019-10-09

Shan K, Qu H, Zhou K, et al (2019)

Distinct Gut Microbiota Induced by Different Fat-to-Sugar-Ratio High-Energy Diets Share Similar Pro-obesity Genetic and Metabolite Profiles in Prediabetic Mice.

mSystems, 4(5): pii:4/5/e00219-19.

Gut microbiota play important roles in host metabolism, especially in diabetes. However, why different diets lead to similar diabetic states despite being associated with different microbiota is not clear. Mice were fed two high-energy diets (HED) with the same energy density but different fat-to-sugar ratios to determine the associations between the microbiota and early-stage metabolic syndrome. The two diets resulted in different microbiota but similar diabetic states. Interestingly, the microbial gene profiles were not significantly different, and many common metabolites were identified, including l-aspartic acid, cholestan-3-ol (5β, 3α), and campesterol, which have been associated with lipogenesis and inflammation. Our study suggests that different metabolic-syndrome-inducing diets may result in different microbiota but similar microbiomes and metabolomes. This suggests that the metagenome and metabolome are crucial for the prognosis and pathogenesis of obesity and metabolic syndrome.IMPORTANCE Various types of diet can lead to type 2 diabetes. The gut microbiota in type 2 diabetic patients are also different. So, two questions arise: whether there are any commonalities between gut microbiota induced by different pro-obese diets and whether these commonalities lead to disease. Here we found that high-energy diets with two different fat-to-sugar ratios can both cause obesity and prediabetes but enrich different gut microbiota. Still, these different gut microbiota have similar genetic and metabolite compositions. The microbial metabolites in common between the diets modulate lipid accumulation and macrophage inflammation in vivo and in vitro This work suggests that studies that only use 16S rRNA amplicon sequencing to determine how the microbes respond to diet and associate with diabetic state are missing vital information.

RevDate: 2019-10-08

Millán-Aguiñaga N, Soldatou S, Brozio S, et al (2019)

Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential.

Microbiology (Reading, England) [Epub ahead of print].

Polar and subpolar ecosystems are highly vulnerable to global climate change with consequences for biodiversity and community composition. Bacteria are directly impacted by future environmental change and it is therefore essential to have a better understanding of microbial communities in fluctuating ecosystems. Exploration of Polar environments, specifically sediments, represents an exciting opportunity to uncover bacterial and chemical diversity and link this to ecosystem and evolutionary parameters. In terms of specialized metabolite production, the bacterial order Actinomycetales, within the phylum Actinobacteria are unsurpassed, producing 10 000 specialized metabolites accounting for over 45 % of all bioactive microbial metabolites. A selective isolation approach focused on spore-forming Actinobacteria of 12 sediment cores from the Antarctic and sub-Arctic generated a culture collection of 50 strains. This consisted of 39 strains belonging to rare Actinomycetales genera including Microbacterium, Rhodococcus and Pseudonocardia. This study used a combination of nanopore sequencing and molecular networking to explore the community composition, culturable bacterial diversity, evolutionary relatedness and specialized metabolite potential of these strains. Metagenomic analyses using MinION sequencing was able to detect the phylum Actinobacteria across polar sediment cores at an average of 13 % of the total bacterial reads. The resulting molecular network consisted of 1652 parent ions and the lack of known metabolite identification supports the argument that Polar bacteria are likely to produce previously unreported chemistry.

RevDate: 2019-10-08

Colman DR, Lindsay MR, Amenabar MJ, et al (2019)

The Intersection of Geology, Geochemistry, and Microbiology in Continental Hydrothermal Systems.

Astrobiology [Epub ahead of print].

Decompressional boiling of ascending hydrothermal waters and separation into a vapor (gas) and a liquid phase drive extensive variation in the geochemical composition of hot spring waters. Yet little is known of how the process of phase separation influences the distribution of microbial metabolisms in springs. Here, we determined the variation in protein coding genes in 51 metagenomes from chemosynthetic hot spring communities that span geochemical gradients in Yellowstone National Park. The 51 metagenomes could be divided into 5 distinct groups that correspond to low and high temperatures and acidic and circumneutral/alkaline springs. A fifth group primarily comprised metagenomes from springs with moderate acidity and that are influenced by elevated volcanic gas input. Protein homologs putatively involved in the oxidation of sulfur compounds, a process that leads to acidification of spring waters, in addition to those involved in the reduction of sulfur compounds were enriched in metagenomes from acidic springs sourced by vapor phase gases. Metagenomes from springs with evidence for elevated volcanic gas input were enriched in protein homologs putatively involved in oxidation of those gases, including hydrogen and methane. Finally, metagenomes from circumneutral/alkaline springs sourced by liquid phase waters were enriched in protein homologs putatively involved in heterotrophy and respiration of oxidized nitrogen compounds and oxygen. These results indicate that the geological process of phase separation shapes the ecology of thermophilic communities through its influence on the availability of nutrients in the form of gases, solutes, and minerals. Microbial acidification of hot spring waters further influences the kinetic and thermodynamic stabilities of nutrients and their bioavailability. These data therefore provide an important framework to understand how geological processes have shaped the evolutionary history of chemosynthetic thermophiles and how these organisms, in turn, have shaped their geochemical environments.

RevDate: 2019-10-08

Zhang HC, Zhang QR, Ai JW, et al (2019)

The role of bone marrow metagenomics next-generation sequencing to differential diagnosis among visceral leishmaniasis, histoplasmosis, and talaromycosis marneffei.

RevDate: 2019-10-08

Breton S, Jouhet J, Guyet U, et al (2019)

Unveiling membrane thermoregulation strategies in marine picocyanobacteria.

The New phytologist [Epub ahead of print].

The wide latitudinal distribution of marine Synechococcus cyanobacteria partly relies on the differentiation of lineages adapted to distinct thermal environments. Membranes are highly thermosensitive cell components and the ability to modulate their fluidity can be critical for the fitness of an ecotype in a particular thermal niche. We compared the thermophysiology of Synechococcus strains representative of major temperature ecotypes in the field. We measured growth, photosynthetic capacities and membrane lipidome variations. We carried out a metagenomic analysis of stations of the Tara Oceans expedition to describe the latitudinal distribution of the lipid desaturase genes in the oceans. All strains maintained efficient photosynthetic capacities over their different temperature growth ranges. Subpolar and cold temperate strains showed enhanced capacities of lipid monodesaturation at low temperature thanks to an additional, poorly regiospecific Δ9-desaturase. In contrast, tropical and warm temperate strains displayed moderate monodesaturation capacities but high proportions of double unsaturations in response to cold, thanks to regiospecific Δ12-desaturases. The desaturase genes displayed specific distributions directly related to latitudinal variations in ocean surface temperature. This study highlights the critical importance of membrane fluidity modulation by desaturases in the adaptive strategies of Synechococcus cyanobacteria during the colonization of novel thermal niches.

RevDate: 2019-10-08

Anonymous (2019)

Correction for Sotoudeh et al., Effects of the peer metagenomic environment on smoking behavior.

Proceedings of the National Academy of Sciences of the United States of America pii:1916279116 [Epub ahead of print].

RevDate: 2019-10-07

Salah M, Azab M, Ramadan A, et al (2019)

New Insights on Obesity and Diabetes from Gut Microbiome Alterations in Egyptian Adults.

Omics : a journal of integrative biology, 23(10):477-485.

Obesity and diabetes are reaching epidemic levels globally. Metagenomics and microbiome science have recently emerged as new tools for studying common complex human diseases. We report in this study notable differences in gut microbiome in adult patients with obesity and diabetes in Egypt. The experimental design was based on comparisons of four study groups: (1) Controls (C) with a normal body mass index, without obesity or diabetes, (2) Obese adults (O) without diabetes, (3) adults with diabetes (D) who are not obese, and (4) Adults who are both obese and diabetic (OD). In a total study sample of 60 participants, we sequenced the 16S ribosomal RNA (rRNA) gene using the Illumina MiSeq platform. Alpha diversity analysis revealed greater diversity in bacterial communities of (D) than controls. Phylum-level analysis identified a trend for overrepresentation of Bacteroidetes (p < 0.07) in (O) and (D) than controls. The ratio of Firmicutes/Bacteroidetes (F/B) displayed a remarkable increase in (OD) than controls. At genus level, Faecalibacterium (p < 0.05) and Akkermansia (p < 0.001) distinguished (O) from controls, while Fusobacterium (p < 0.001) and Bacteroides (p < 0.001) was significantly more abundant in (OD) compared with D. Surprisingly, isoquinoline, quinone and ubiquinone alkaloid biosynthesis were overrepresented in controls compared with other three study groups. Presumably, the latter observation might potentially suggest an antihyperglycemic activity of the gut microbiota. In conclusion, the health state of the adults in our study defined the composition of the gut microbiota. Moreover, obesity and diabetes were associated with remarkably enriched populations of Firmicutes and Bacteroidetes. The abundance of Fusobacterium is worth further research and exploration as a candidate biomarker for prediabetes especially in obese individuals. The potential antihyperglycemic activity of the gut microbiota is also noteworthy for future studies in other world populations.

RevDate: 2019-10-07

Ye L, Das P, Li P, et al (2019)

Carbohydrate active enzymes are affected by diet transition from milk to solid food in infant gut microbiota.

FEMS microbiology ecology pii:5582603 [Epub ahead of print].

Infants experience a dramatic change in their food in the first year after birth when they shift from breast milk to solid food. This results in a large change in presence of indigestible polysaccharides, a primary energy resource of gut microbes. How the gut microbiota adapts to this dietary shift has not been well examined. Here by using metagenomics data, we studied carbohydrate-active enzymes (CAZymes) of gut microbiota, which are essential enzymes catalyzing the breakdown of polysaccharides, during this dietary shift. We developed a new approach to categorize CAZyme families by food intake and found CAZyme families associated with milk or solid food. We also found CAZymes with most abundance in 12 months infants are not associated with solid food or milk, but may be related to modulating carbohydrates in the mucus. Additionally, the abundance of gut CAZymes were found to be affected by many other factors, including delivery modes and life style in adults. Taken together, our findings provide novel insights into the dynamic change of gut CAZymes in early human life and provide potential markers for food interference or gut microbiota restoration.

RevDate: 2019-10-07

Takhar JS, Doan TA, JA Gonzales (2019)

Primary vitreoretinal lymphoma: empowering our clinical suspicion.

Current opinion in ophthalmology, 30(6):491-499.

PURPOSE OF REVIEW: Vitreoretinal lymphoma (VRL) is well known as a masquerade syndrome. However, delays in diagnosis are common particularly because of the small volume of tissue that is used for investigative studies. We outline the current diagnostic tests available to clinicians and provide a glimpse of possible future novel diagnostics.

RECENT FINDINGS: The use of spectral domain ocular coherence tomography to identify subretinal lesions has proven to be a reliable ally to clinicians. Nevertheless, the diagnostic gold standard remains cytology, which requires a skilled pathologist. Molecular tests, including MYD88 polymerase chain reaction testing has further refined our diagnostic capabilities. Metagenomic deep sequencing is a newer molecular test that offers the ability to identify any mutation associated with lymphoma development and may offer more sensitive testing in the future.

SUMMARY: Clinicians have developed a strong acumen for suspecting VRL based upon clinical features, which can further be supported by a variety of imaging modalities. Delays in diagnosis continue to occur particularly because of the small volume of ocular fluid available for testing and because current tests offer a biased approach in terms of limited scope of detecting a specific mutation or cytopathologic feature(s). Newer molecular techniques feature an expanded scope of detecting any mutation associated with lymphomatous development.

RevDate: 2019-10-07

Huang ZS, Wei Z, Xiao XL, et al (2019)

Biooxidation of Elemental Mercury into Mercury Sulfide and Humic Acid Bound Mercury by Sulfate Reduction for Hg0 Removal in Flue Gas.

Environmental science & technology [Epub ahead of print].

Bioconversion of elemental mercury (Hg0) into immobile, non-toxic and less bioavailable species is of vital environmental significance. Here, we investigated bioconversion of Hg0 in a sulfate-reducing membrane biofilm reactor (MBfR). MBfR achieved effective Hg0 removal by sulfate bio-reduction.16 S rDNA sequencing and metagenomic sequencing revealed that diverse groups of mercury-oxidizing/sulfate-reducing bacteria (Desulfobulbus, Desulfuromonas, Desulfomicrobium and etc.) utilized Hg0 as initial electron donor and sulfate as terminal electron acceptor to form the overall redox, these microorganisms could couple mercury bio-oxidation to sulfate bio-reduction. Analysis on mercury speciation in biofilm by sequential extraction processes (SEPs) and inductively coupled mass spectrometry (ICP-MS) and mercury temperature programmed desorption (Hg-TPD) showed that mercury sulfide (HgS) and humic acid bound mercury (HA-Hg) were two major products of Hg0 bio-oxidation. With HgS and HA-Hg comprehensively characterized by X-ray diffraction (XRD), excitation-emission matrix spectra (EEM), scanning electron microscopy-energy disperse spectroscopy (SEM-EDS), X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR), it was proposed that biologically oxidized mercury (Hg2+) further reacted with biogenic sulfides to form cubically crystallized metacinnbar (β-HgS) extracellular particles. Hg2+ was also complexed with functional groups -SH, -OH, -NH- and -COO- in humic acids from extracellular polymeric substances (EPS) to form HA-Hg. HA-Hg may further react with biogenic sulfides to form HgS. Bioconversion of Hg0 into HgS was therefore achieved and can be a feasible biotechnique for flue gas demercuration.

RevDate: 2019-10-07

Zhao F, Zhou G, Liu X, et al (2019)

Dietary Protein Sources Differentially Affect the Growth of Akkermansia muciniphila and Maintenance of the Gut Mucus Barrier in Mice.

Molecular nutrition & food research [Epub ahead of print].

SCOPE: The gut microbiota plays an essential role in linking diet to host health. The specific role of different dietary proteins on the gut microbiota and health is less understood. Here we investigated the impact of proteins derived from chicken and soy on the gut microbiota and host gut barrier in C57BL/6 mice.

METHODS AND RESULTS: Specific-pathogen-free and germ-free mice were assigned to either a chicken or a soy protein-based diet for 4 weeks. Compared with a chicken protein-based diet, intake of a soy protein-based diet reduced the abundance of A. muciniphila and the number of goblet cells, lowered the level of Muc2 mRNA, and decreased the thickness of the mucus layer in the colon of specific-pathogen-free mice. In germ-free mice colonization with A. muciniphila combined with intake of a chicken protein-based diet resulted in a higher expression of the Muc2 mRNA in colon, and surprisingly, an increased potential for oxidative phosphorylation in A. muciniphila compared with colonized mice fed a soy protein-based diet.

CONCLUSION: These findings suggest possible mutually beneficial interactions between the growth and function of A. muciniphila and host mucus barrier in response to intake of a chicken protein-based diet contrasting the intake of a soy protein-based diet. This article is protected by copyright. All rights reserved.

RevDate: 2019-10-07

Khalid NA, Rajandas H, Parimannan S, et al (2019)

Insights into microbial community structure and diversity in oil palm waste compost.

3 Biotech, 9(10):364.

Empty fruit bunch (EFB) and palm oil mill effluent (POME) are the major wastes generated by the oil palm industry in Malaysia. The practice of EFB and POME digester sludge co-composting has shown positive results, both in mitigating otherwise environmentally damaging waste streams and producing a useful product (compost) from these streams. In this study, the bacterial ecosystems of 12-week-old EFB-POME co-compost and POME biogas sludge from Felda Maokil, Johor were analysed using 16S metagenome sequencing. Over ten phyla were detected, with Chloroflexi being the predominant phylum, representing approximately 53% of compost and 23% of the POME microbiome reads. The main bacterial lineage found in the compost and POME was Anaerolinaceae (Chloroflexi) with 30% and 18% of the total gene fragments, respectively. The significant differences between compost and POME communities were abundances of Syntrophobacter, Sulfuricurvum and Coprococcus. No methanogens were identified due to the bias in general 16S primers to eubacteria. The preponderance of anaerobic species in the compost and high abundance of secondary metabolite fermenting bacteria is due to an extended composting time, with anaerobic collapse of the pile due to the tropical heat. Predictive functional profiles of the metagenomes using 16S rRNA marker genes suggest that the presence of enzymes involved in degradation of polysaccharides such as glucoamylase, endoglucanase and arabinofuranosidase, all of which were strongly active in POME. Eubacterial species associated with cellulytic methanogenesis were present in both samples.

RevDate: 2019-10-07

Galvão KN, Bicalho RC, SJ Jeon (2019)

Symposium review: The uterine microbiome associated with the development of uterine disease in dairy cows.

Journal of dairy science pii:S0022-0302(19)30868-9 [Epub ahead of print].

Until 2010, our knowledge of the uterine microbiome in cows that developed uterine disease relied almost exclusively on culture-dependent studies and mostly included cows with clinical endometritis (i.e., with purulent uterine discharge). Those studies consistently found a strong positive correlation between Trueperella pyogenes and clinical endometritis, whereas other pathogens such as Escherichia coli, Fusobacterium necrophorum, Prevotella melaninogenica, and Bacteroides spp. were also commonly cocultured. In contrast, Streptococcus spp., Staphylococcus spp., and Bacillus spp. were usually isolated from healthy cows. Starting in 2010, culture-independent studies using PCR explored the microbiome of cows with metritis and clinical endometritis, and observed that E. coli was a pioneer pathogen that predisposed cows to infection with F. necrophorum, which was strongly associated with metritis, and to infection with T. pyogenes, which was strongly associated with clinical endometritis. Starting in 2011, culture-independent studies using metagenomic sequencing expanded our knowledge of the uterine microbiome. It has been shown that cows have bacteria in the uterus even before calving, they have an established uterine microbiome within 20 min of calving, and that the microbiome structure is identical between cows that develop metritis and healthy cows until 2 d postpartum, after which the bacterial structure of cows that developed metritis deviates in favor of greater relative abundance of Bacteroidetes and Fusobacteria and lesser relative abundance of Proteobacteria and Tenericutes. The shift in the uterine microbiome in cows that develop metritis is characterized by a loss of heterogeneity and a decrease in bacterial richness. At the genus level, Bacteroides, Porphyromonas, and Fusobacterium have the strongest association with metritis. At the species level, we observed that Bacteroides pyogenes, Porphyromonas levii, and Helcococcus ovis were potential emerging uterine pathogens. Finally, we have shown that the hematogenous route is a viable route of uterine infection with uterine pathogens. Herein, we propose that metritis is associated with a dysbiosis of the uterine microbiota characterized by decreased richness, and an increase in Bacteroidetes and Fusobacteria, particularly Bacteroides, Porphyromonas, and Fusobacterium.

RevDate: 2019-10-07

Keeling PJ (2019)

Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 374(1786):20190085.

Microbial eukaryotes (protists) are structurally, developmentally and behaviourally more complex than their prokaryotic cousins. This complexity makes it more difficult to translate genomic and metagenomic data into accurate functional inferences about systems ranging all the way from molecular and cellular levels to global ecological networks. This problem can be traced back to the advent of the cytoskeleton and endomembrane systems at the origin of eukaryotes, which endowed them with a range of complex structures and behaviours that still largely dominate how they evolve and interact within microbial communities. But unlike the diverse metabolic properties that evolved within prokaryotes, the structural and behavioural characteristics that strongly define how protists function in the environment cannot readily be inferred from genomic data, since there is generally no simple correlation between a gene and a discrete activity or function. A deeper understanding of protists at both cellular and ecological levels, therefore, requires not only high-throughput genomics but also linking such data to direct observations of natural history and cell biology. This is challenging since these observations typically require cultivation, which is lacking for most protists. Potential remedies with current technology include developing a more phylogenetically diverse range of model systems to better represent the diversity, as well as combining high-throughput, single-cell genomics with microscopic documentation of the subject cells to link sequence with structure and behaviour. This article is part of a discussion meeting issue 'Single cell ecology'.

RevDate: 2019-10-07

Santoro AE, Kellom M, SM Laperriere (2019)

Contributions of single-cell genomics to our understanding of planktonic marine archaea.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 374(1786):20190096.

Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes-the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening. This article is part of a discussion meeting issue 'Single cell ecology'.

RevDate: 2019-10-07

Needham DM, Poirier C, Hehenberger E, et al (2019)

Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 374(1786):20190086.

Giant viruses have remarkable genomic repertoires-blurring the line with cellular life-and act as top-down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four 'PacV' partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant Mimiviridae, incorporating the Cafeteria roenbergensis virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (e-value < 10-5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence-absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs. This article is part of a discussion meeting issue 'Single cell ecology'.

RevDate: 2019-10-03

Ma A, Sun M, McDermaid A, et al (2019)

MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.

Bioinformatics (Oxford, England) pii:5580590 [Epub ahead of print].

RevDate: 2019-10-07
CmpDate: 2019-10-07

González-Escobar JL, Grajales-Lagunes A, Smoliński A, et al (2018)

Microbiota of edible Liometopum apiculatum ant larvae reveals potential functions related to their nutritional value.

Food research international (Ottawa, Ont.), 109:497-505.

Edible insects, due to their high nutritive value, are currently considered as a potential renewable source for food and feed production. Liometopum apiculatum ants are widely distributed in arid and semi-arid ecosystems and their larvae (escamoles) are considered as a delicacy, however the microbial importance in L. apiculatum nutritional ecology is unknown. The aim of this research was to characterize the microorganisms associated with both L. apiculatum larvae and the reproductive adult ants using the 16S rRNA gene sequencing and culturomics approaches. The obligate endosymbionts were also investigated through microscopic analysis. The most abundant Phylum identified by sequencing in the larvae was Firmicutes while in adult ants was Proteobacteria. Interestingly, the culturomics results showed 15 genera corresponding to the bacteria identified by sequencing analysis. Particularly, it was observed a large population of nitrogen-fixing bacteria, which could be linked with the high protein content in escamoles. Endosymbionts were detected in bacteoriocytes, these bacteria are related with vitamins and essential amino acids biosynthesis, and both compounds contributing to the high nutritional value of escamoles. This is the first report of the microorganisms present in the escamolera ant ensuring their safety as food and opening new areas of nutritional ecological and food processing.

RevDate: 2019-10-07
CmpDate: 2019-10-04

Ndou SP, Tun HM, Kiarie E, et al (2018)

Dietary supplementation with flaxseed meal and oat hulls modulates intestinal histomorphometric characteristics, digesta- and mucosa-associated microbiota in pigs.

Scientific reports, 8(1):5880.

The establishment of a healthy gastrointestinal milieu may not only offer an opportunity to reduce swine production costs but could also open the way for a lifetime of human health improvement. This study investigates the effects of feeding soluble fibre from flaxseed meal-containing diet (FM) and insoluble fibre from oat hulls-containing diet (OH) on histomorphological characteristics, digesta- and mucosa-associated microbiota and their associations with metabolites in pig intestines. In comparison with the control (CON) and OH diets, the consumption of FM increased (P < 0.001) the jejunal villi height (VH) and the ratio of VH to crypt depths. The PERMANOVA analyses showed distinct (P < 0.05) microbial communities in ileal digesta and mucosa, and caecal mucosa in CON and FM-diets fed pigs compared to the OH diet-fed pigs. The predicted functional metagenomes indicated that amino acids and butanoate metabolism, lysine degradation, bile acids biosynthesis, and apoptosis were selectively enhanced at more than 2.2 log-folds in intestinal microbiota of pigs fed the FM diet. Taken together, flaxseed meal and oat hulls supplementation in growing pigs' diets altered the gastrointestinal development, as well as the composition and function of microbial communities, depending on the intestinal segment and physicochemical property of the dietary fibre source.

RevDate: 2019-10-07
CmpDate: 2019-10-03

Sun T, Wang XQ, Zhao ZL, et al (2018)

A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota.

Scientific reports, 8(1):5324.

The Chinese white wax scale insect (Ericerus pela) is an economically valuable species with an important role in wax production. Recently, in a greenhouse in Kunming, we identified a genus of fungus that infects and kills E. pela females. This study sought to perform the molecular detection of entomopathogens and analyze the changes in the host microbiota after entomopathogen infection. We used library construction, high-throughput sequencing and real-time quantitative polymerase chain reaction (RT-qPCR) to identify the fungi infecting adult E. pela, to understand the changes in the host organism, and to determine the distribution of the entomopathogens. Cladosporium langeronii and C. sphaerospermum were the main pathogenic species that infected the E. pela females, and they were most prevalent in the dorsal cuticle. In vivo, after infection, the proportion of Cladosporium clearly increased. The infection had little influence on the fungal community but had a strong influence on the bacterial community. After infection, Arsenophonus was dominant, and numerous bacterial genera disappeared. However, Rickettsia, instead of Arsenophonus, became dominant in the Cladosporium-infected individuals that had also been infected with Rickettsia. We identified the species that infected E. pela females and determined the influence of infection on the host microorganisms.

RevDate: 2019-10-07
CmpDate: 2019-10-03

Wang X, Wang Z, Jiang P, et al (2018)

Bacterial diversity and community structure in the rhizosphere of four Ferula species.

Scientific reports, 8(1):5345.

The medicinal value of the Ferula L. has been recognized for more than a thousand years. Wild stocks of Ferula have declined dramatically because high economic value has led to overharvesting. The objective of this study was to compare the rhizosphere microbial community of four Ferula species [F. syreitschikowii K.-Pol., F. gracilis (Ledeb.) Ledeb., F. ferulaeoides (Steud.) Korov., and F. lehmannii Boiss.] in the northern part of Xinjiang, China. The 16S rRNA sequences of rhizosphere bacteria were obtained with an Illumina paired-end sequence platform. Analysis was conducted to determine the richness and diversity of the rhizosphere bacterial communities. Two-way ANOVA indicated that plant species and soil depth had no significant effect on the alpha diversity of rhizobacteria. Linear discriminant analysis effect size showed that F. lehmannii followed by F. ferulaeoides had the most biomarkers and the highest taxon level, F. syreitschikowii and F. gracilis the least, while F. syreitschikowii and F. gracilis had the least property. This trend is consistent with reports that the medicinal value of F. lehmannii and F. ferulaeoides is greater than that of F. gracilis and F. syreitschikowii. The results of this study provide information that could be used for the commercial cultivation of Ferula spp.

RevDate: 2019-10-05

Cox SR, Lindsay JO, Fromentin S, et al (2019)

Effects of Low-FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial.

Gastroenterology pii:S0016-5085(19)41366-8 [Epub ahead of print].

BACKGROUND & AIMS: There is limited evidence that a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) reduces gut symptoms in quiescent inflammatory bowel disease (IBD). We performed a randomized, controlled trial to investigate the effects of a low-FODMAP diet on persistent gut symptoms, the intestinal microbiome, and circulating markers of inflammation in patients with quiescent IBD.

METHODS: We performed a single-blind trial of 52 patients with quiescent Crohn's disease or ulcerative colitis and persistent gut symptoms at 2 large gastroenterology clinics in the United Kingdom. Patients were randomly assigned to groups that followed a diet low in FODMAPs (n=27) or a control diet (n=25), with dietary advice, for 4 weeks. Gut symptoms and health-related quality of life were measured using validated questionnaires. Stool and blood samples were collected at baseline and end of trial. We assessed fecal microbiome composition and function using shotgun metagenomic sequencing and phenotypes of T cells in blood using flow cytometry.

RESULTS: A higher proportion of patients reported adequate relief of gut symptoms following the low-FODMAP diet (14/27, 52%) than the control diet (4/25, 16%, P=.007). Patients had a greater reduction in irritable bowel syndrome severity scores following the low-FODMAP diet (mean reduction of 67; standard error, 78) than the control diet (mean reduction of 34; standard error, 50), although this difference was not statistically significant (P=.075). Following the low-FODMAP diet, patients had higher health-related quality of life scores (81.9±1.2) than patients on the control diet (78.3±1.2, P=.042). A targeted analysis revealed that in stool samples collected at the end of the study period, patients on the low-FODMAP diet had significantly lower abundance of Bifidobacterium adolescentis, B longum, and Faecalibacterium prausnitzii than patients on control diet. However, microbiome diversity and markers of inflammation did not differ significantly between groups.

CONCLUSIONS: In a trial of the low-FODMAP diet vs a control diet in patients with quiescent IBD, we found no significant difference after 4 weeks in change in irritable bowel syndrome severity scores, but significant improvements in specific symptom scores and numbers reporting adequate symptom relief. The low-FODMAP diet reduced fecal abundance of microbes believed to regulate the immune response, compared with the control diet, but had no significant effect on markers of inflammation. We conclude that a 4-week diet low in FODMAPs is safe and effective for managing persistent gut symptoms in patients with quiescent IBD. no: ISRCTN17061468.

RevDate: 2019-10-05

Peña-Gonzalez A, Soto-Girón MJ, Smith S, et al (2019)

Metagenomic signatures of gut infection caused by different Escherichia coli pathotypes.

Applied and environmental microbiology pii:AEM.01820-19 [Epub ahead of print].

Escherichia coli is a leading contributor to infectious diarrhea and child mortality worldwide but it remains unknown how alterations in the gut microbiome vary for distinct E. coli pathotypes and whether these signatures can be used for diagnostic purposes. Further, the majority of enteric diarrheal infections are not diagnosed with respect to their etiological agent(s) due to technical challenges. Towards addressing these issues, we devised a novel approach that combined traditional, isolate-based and molecular biology techniques with metagenomics analysis of stool samples and epidemiological data. Application of this pipeline to children enrolled in a case-control study of diarrhea in Ecuador showed that, in about half of the cases where an E. coli pathotype was detected by culture and PCR, E. coli was likely not the causative agent based on metagenomic-derived low relative abundance, level of clonality and/or virulence gene content. Our results also showed that diffuse adherent E. coli (DAEC), a pathotype that is generally underrepresented in previous studies of diarrhea and thus, thought to not be highly virulent, caused several small-scale diarrheal outbreaks across a rural to urban gradient in Ecuador. DAEC infections were uniquely accompanied by co-elution of high amounts of human DNA and conferred significant shifts in the gut microbiome composition relative to controls or infections caused by other E. coli pathotypes. Our study shows that diarrheal infections can be efficiently diagnosed for their etiological agent and categorized based on their effects on the gut microbiome using metagenomic tools, which opens new possibilities for diagnostics and treatment.ImportanceE. coli infectious diarrhea is an important contributor to child mortality worldwide. However, diagnosing and thus, treating E. coli infections remains challenging due to technical and other reasons associated with the limitations of the traditional culture-based techniques and the requirement to apply Koch's postulates. In this study, we integrated traditional microbiology techniques with metagenomics and epidemiology data in order to identify cases of diarrhea where E. coli was most likely the causative disease agent and evaluate specific signatures in the disease-state gut microbiome that distinguish between DAEC, ETEC and EPEC E. coli pathotypes. Therefore, our methodology and results should be highly relevant for diagnosing and treating diarrheal infections, and have important applications in public health.

RevDate: 2019-10-05

Wang B, XL Wang (2019)

Species diversity of fecal microbial flora in Canis lupus familiaris infected with canine parvovirus.

Veterinary microbiology, 237:108390.

Parvovirosis is a highly contagious disease in dogs, often causing acute hemorrhagic enteritis and altering the intestinal microflora. In this study, real-time PCR was used to detect the viral copy numbers in dogs diagnosed with the disease. Hematological and hemobiochemical parameters were also determined. The species and abundances of the fecal microbial flora in both sick and healthy dogs were determined and compared via metagenomic sequencing. The viral copy numbers in the sick dogs were infected with little difference in the positive samples. The blood coagulation time was significantly shorter and the number of white blood cells was significantly greater in the sick dogs. The serum calcium content was slightly increased and the phosphorus content was reduced in the sick dogs. The LDH and CK activities were significantly elevated in the sick dogs. Metagenomic sequencing and analysis revealed relatively more Escherichia, Lachnoclostridium, gnavus group (Ruminococcus), and uncultured_bacterium_f_lachnospiraceae in the infected dogs, whereas the abundance of Collinsella was relatively reduced. Alloprevotella and Sutterella were absent among the fecal microorganisms of the infected dogs. The relative abundances of Romboutsia, Erysipelatoclostridium, Anaerotruncus, and Blautia were significantly increased in the infected dogs. Functional analysis of the metagenomes of the samples indicated a significant enrichment of the 'replication, recombination and repair', 'nucleotide transport and metabolism', 'transcription', and 'defense metabolism' functions in the fecal microbial flora of the infected dogs. In summary, this study provides a scientific theoretical basis for preventing and controlling diarrhea caused by the canine parvovirus.


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
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

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 )