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PLOS Computational Biology: Translational Bioinformatics

PLOS Computational Biology: Translational Bioinformatics | Bioinformatics and holobiota | Scoop.it
PLOS Collections: Article collections published by the Public Library of Science
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Free book - overview of modern bioinformatics

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Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota | Bioinformatics and holobiota | Scoop.it
Highlights

 

Diet reproducibly alters the gut microbiota of mice with diverse genotypes

The gut microbiota exhibits a linear dose response to dietary perturbations

Postperturbation, most bacterial taxa reach a new steady state in 3 days

Most changes are reversible, but some taxa reflect prior diets (hysteresis)

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Potential of fecal microbiota for early-stage detection of colorectal cancer- Molecular Systems Biology

Potential of fecal microbiota for early-stage detection of colorectal cancer- Molecular Systems Biology | Bioinformatics and holobiota | Scoop.it

Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved > 45% relative to the FOBT, while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early- and late-stage cancer and could be validated in independent patient and control populations (N = 335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host–microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients, accompanied by an increase of lipopolysaccharide metabolism

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Assessment of quality control approaches for metagenomic data analysis : Scientific Reports : Nature Publishing Group

Assessment of quality control approaches for metagenomic data analysis : Scientific Reports : Nature Publishing Group | Bioinformatics and holobiota | Scoop.it

Results based on both simulated and real metagenomic datasets have shown that: firstly, QC-Chain is superior in its ability for contamination identification for metagenomic NGS datasets with different complexities with high sensitivity and specificity.

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Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile | Bioinformatics and holobiota | Scoop.it

Here we correlate loss of specific bacterial taxa with development of infection, by treating mice with different antibiotics that result in distinct microbiota changes and lead to varied susceptibility to C. difficile. Mathematical modelling augmented by analyses of the microbiota of hospitalized patients identifies resistance-associated bacteria common to mice and humans. Using these platforms, we determine that Clostridium scindens, a bile acid 7[agr]-dehydroxylating intestinal bacterium, is associated with resistance to C. difficile infection and, upon administration, enhances resistance to infection in a secondary bile acid dependent fashion. Using a workflow involving mouse models, clinical studies, metagenomic analyses, and mathematical modelling, we identify a probiotic candidate that corrects a clinically relevant microbiome deficiency.

Alexander Tyakht's insight:

math. modeling, antibiotics, expreimental mice

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Microbiome | Full text | LotuS: an efficient and user-friendly OTU processing pipeline

16S ribosomal DNA (rDNA) amplicon sequencing is frequently used to analyse the structure of bacterial communities from oceans to the human microbiota. However, computational power is still a major bottleneck in the analysis of continuously enlarging metagenomic data sets. Analysis is further complicated by the technical complexity of current bioinformatics tools.
Alexander Tyakht's insight:

kind of new Qiime from EMBL, MiSeq supported

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Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness | Bioinformatics and holobiota | Scoop.it

We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus andStaphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candida taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a “commensal lifestyle.”

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Experimental evaluation of distorted communities that resemble what we see in our samples from ICU kids. 

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Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae

We isolated a repertoire of carbapenemase-encoding Enterobacteriaceae, including multiple strains of Klebsiella pneumoniae, Klebsiella oxytoca, Escherichia coli, Enterobacter cloacae, Citrobacter freundii, and Pantoea species. Long-read genome sequencing with full end-to-end assembly revealed that these organisms carry the carbapenem resistance genes on a wide array of plasmids. K. pneumoniae and E. cloacaeisolated simultaneously from a single patient harbored two different carbapenemase-encoding plasmids, indicating that plasmid transfer between organisms was unlikely within this patient. We did, however, find evidence of horizontal transfer of carbapenemase-encoding plasmids between K. pneumoniae, E. cloacae, and C. freundii in the hospital environment. Our data, including full plasmid identification, challenge assumptions about horizontal gene transfer events within patients and identify possible connections between patients and the hospital environment. 

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Plasmids as the carriers of AR

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Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates

Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates | Bioinformatics and holobiota | Scoop.it

The gut microbiota of a healthy person may not be equivalent to a healthy microbiota. It is possible that the Western microbiota is actually dysbiotic and predisposes individuals to a variety of diseases. The asymmetric plasticity between the relatively stable human genome and the more malleable gut microbiome suggests that incompatibilities between the two could rapidly arise. The Western lifestyle, which includes a diet low in microbiota-accessible carbohydrates (MACs), has selected for a microbiota with altered membership and functionality compared to those of groups living traditional lifestyles. Interactions between resident microbes and host leading to immune dysregulation may explain several diseases that share inflammation as a common basis. The low-MAC Western diet results in poor production of gut microbiota-generated short-chain fatty acids (SCFAs), which attenuate inflammation through a variety of mechanisms in mouse models. Studies focused on modern and traditional societies, combined with animal models, are needed to characterize the connection between diet, microbiota composition, and function. Differentiating between an optimal microbiota, one that increases disease risk, and one that is causative or potentiates disease will be required to further understand both the etiology and possible treatments for health problems related to microbiota dysbiosis.

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Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads | Bioinformatics and holobiota | Scoop.it

To assess the functional capacities of microbial communities, including those inhabiting the human body, shotgun metagenomic reads are often aligned to a database of known genes. Such homology-based annotation practices critically rely on the assumption that short reads can map to orthologous genes of similar function. This assumption, however, and the various factors that impact short read annotation, have not been systematically evaluated. To address this challenge, we generated an extremely large database of simulated reads (totaling 15.9 Gb), spanning over 500,000 microbial genes and 170 curated genomes and including, for many genomes, every possible read of a given length. We annotated each read using common metagenomic protocols, fully characterizing the effect of read length, sequencing error, phylogeny, database coverage, and mapping parameters. We additionally rigorously quantified gene-, genome-, and protocol-specific annotation biases. Overall, our findings provide a first comprehensive evaluation of the capabilities and limitations of functional metagenomic annotation, providing crucial goal-specific best-practice guidelines to inform future metagenomic research.


Alexander Tyakht's insight:

issues of metagenomic functional profiling

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Microbiology: Microbiome science needs a healthy dose of scepticism (Nature)

Microbiology: Microbiome science needs a healthy dose of scepticism (Nature) | Bioinformatics and holobiota | Scoop.it

Here are five questions that anyone conducting or evaluating this research should ask to keep from getting carried away by hype.

-Can experiments detect differences that matter?
-Does the study show causation or just correlation? 
-What is the mechanism?
-How much do experiments reflect reality?
-Could anything else explain the results?

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Alterations of the human gut microbiome in liver cirrhosis : Nature

Alterations of the human gut microbiome in liver cirrhosis : Nature | Bioinformatics and holobiota | Scoop.it

iver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate < 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. 

Alexander Tyakht's insight:

mouth bacteria invasion of guts associated with cirrhosis

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Iranian is first woman to nab highest prize in maths

Iranian is first woman to nab highest prize in maths | Bioinformatics and holobiota | Scoop.it
Maryam Mirzakhani is among four young researchers to win Fields Medals, awarded every four years.
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!

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Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification

Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification | Bioinformatics and holobiota | Scoop.it

We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. We tested the program on simulated datasets as well as experimental data from Illumina, IonTorrent, and Roche 454 sequencing platforms. We found that Taxoner performs as well as, and often better than BLAST, but requires two orders of magnitude less running time meaning that it can be run on desktop or laptop computers. 

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Host Demise as a Beneficial Function of Indigenous Microbiota in Human Hosts

Host Demise as a Beneficial Function of Indigenous Microbiota in Human Hosts | Bioinformatics and holobiota | Scoop.it

We hypothesize that the age structure of early humans was maintained by mechanisms incorporating the programmed death of senescent individuals, including by means of interactions with their indigenous microorganisms.

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Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis | Bioinformatics and holobiota | Scoop.it
Intestinal microbiota exhibit diurnal oscillations in composition and function

Feeding rhythms direct microbiota oscillations

Chronic jet lag is associated with loss of microbiota rhythms and dysbiosis

Jet-lag-associated dysbiosis in mice and humans promotes metabolic imbalances

 

 

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Cell: Human Genetics Shape the Gut Microbiome

Cell: Human Genetics Shape the Gut Microbiome | Bioinformatics and holobiota | Scoop.it

we compared microbiotas across >1,000 fecal samples obtained from the TwinsUK population, including 416 twin pairs. We identified many microbial taxa whose abundances were influenced by host genetics. The most heritable taxon, the family Christensenellaceae, formed a co-occurrence network with other heritable Bacteria and with methanogenic Archaea. Furthermore, Christensenellaceae and its partners were enriched in individuals with low body mass index (BMI). An obese-associated microbiome was amended with Christensenella minuta, a cultured member of the Christensenellaceae, and transplanted to germ-free mice. C. minuta amendment reduced weight gain and altered the microbiome of recipient mice. Our findings indicate that host genetics influence the composition of the human gut microbiome and can do so in ways that impact host metabolism.

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Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization

Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization | Bioinformatics and holobiota | Scoop.it

In this study, we found that dairy cow manure amendment enhanced the proliferation of resident antibiotic-resistant bacteria and genes encoding β-lactamases in soil even though the cows from which the manure was derived had not been treated with antibiotics. Our findings provide previously unidentified insight into the mechanism by which amendment with manure enriches antibiotic-resistant bacteria in soil.

Alexander Tyakht's insight:

sh*t happens

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Dmitry Alexeev's curator insight, October 7, 6:36 AM

antibiotic resistance enrichment after fertilization

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Members of the human gut microbiota involved in recovery from Vibrio cholerae infection

Members of the human gut microbiota involved in recovery from Vibrio cholerae infection | Bioinformatics and holobiota | Scoop.it

Here we conduct a detailed time-series metagenomic study of faecal microbiota collected during the acute diarrhoeal and recovery phases of cholera in a cohort of Bangladeshi adults living in an area with a high burden of disease2. We find that recovery is characterized by a pattern of accumulation of bacterial taxa that shows similarities to the pattern of assembly/maturation of the gut microbiota in healthy Bangladeshi children3. To define the underlying mechanisms, we introduce into gnotobiotic mice an artificial community composed of human gut bacterial species that directly correlate with recovery from cholera in adults and are indicative of normal microbiota maturation in healthy Bangladeshi children3. One of the species, Ruminococcus obeum, exhibits consistent increases in its relative abundance upon V. cholerae infection of the mice. Follow-up analyses, including mono- and co-colonization studies, establish that R. obeum restricts V. cholerae colonization, that R. obeum luxS (autoinducer-2 (AI-2) synthase) expression and AI-2 production increase significantly with V. cholerae invasion, and that R. obeum AI-2 causes quorum-sensing-mediated repression of several V. cholerae colonization factors. Co-colonization with V. cholerae mutants discloses that R. obeum AI-2 reduces Vibrio colonization/pathogenicity through a novel pathway that does not depend on the V. cholerae AI-2 sensor, LuxP. The approach described can be used to mine the gut microbiota of Bangladeshi or other populations for members that use autoinducers and/or other mechanisms to limit colonization with V. cholerae, or conceivably other enteropathogens.

Alexander Tyakht's insight:

metagenomics + experimental gut Ruminococcus vs . Vibrio co-colonization from J. Gordon

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Artificial sweeteners induce glucose intolerance by altering the gut microbiota

Artificial sweeteners induce glucose intolerance by altering the gut microbiota | Bioinformatics and holobiota | Scoop.it

Here we demonstrate that consumption of commonly used NAS formulations drives the development of glucose intolerance through induction of compositional and functional alterations to the intestinal microbiota. These NAS-mediated deleterious metabolic effects are abrogated by antibiotic treatment, and are fully transferrable to germ-free mice upon faecal transplantation of microbiota configurations from NAS-consuming mice, or of microbiota anaerobically incubated in the presence of NAS.

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a hidden influence of industrial diet

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Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.

Alexander Tyakht's insight:

“[In this work] you have a novel approach that is telling you that, still, today, most of the microorganisms inside the human gut have not been characterized, are not known. This is, to me, the lesson in this study”, saidProfessor Francisco Guarner, head of the Experimental Laboratory at the University Hospital Vall d’Hebron(Barcelona), and co-author of both studies.

Interestingly, some of the subjects analysed in the study had very few of these new species. By checking who these individuals were, the authors found that they all had Crohn’s disease, ulcerative colitis, or metabolic syndrome with an inflammatory component. These findings suggest that there is a correlation between suffering from these diseases and having less diversity in these unknown species.

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Modelling the Emergent Dynamics and Major Metabolites of the Human Colonic Microbiota

Modelling the Emergent Dynamics and Major Metabolites of the Human Colonic Microbiota | Bioinformatics and holobiota | Scoop.it

We present here a first attempt at modelling microbial dynamics in the human colon incorporating both uncertainty and adaptation. This is based on the development of a Monod-equation based, differential equation model which produces computer simulations of the population dynamics and major metabolites of microbial communities from the human colon. To reduce the complexity of the system we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways, and its preferred pH range. The model simulates the growth of a large number of bacterial strains and incorporates variation in microbiota composition between people, whilst also allowing succession and enabling adaptation to environmental changes. The model is shown to reproduce many of the observed changes in major phylogenetic groups and key metabolites such as butyrate, acetate and propionate in response to a one unit pH shift in experimental continuous flow fermentors inoculated with human faecal microbiota. Nevertheless, it should be regarded as a learning tool to be updated as our knowledge of bacterial groups and their interactions expands. Given the difficulty of accessing the colon, modelling can play an extremely important role in interpreting experimental data and predicting the consequences of dietary modulation

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Arousal vs. Relaxation: A Comparison of the Neurophysiological and Cognitive Correlates of Vajrayana and Theravada Meditative Practices

Arousal vs. Relaxation: A Comparison of the Neurophysiological and Cognitive Correlates of Vajrayana and Theravada Meditative Practices | Bioinformatics and holobiota | Scoop.it

In conclusion, consistent with Tibetan scriptures that described Shamatha and Vipassana techniques as those that calm and relax the mind, and Vajrayana techniques as those that require ‘an awake quality’ of the mind, we show that Theravada and Vajrayana meditations are based on different neurophysiological mechanisms, which give rise to either a relaxation or arousal response.

Alexander Tyakht's insight:

we guess so

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mynewgut.eu

mynewgut.eu | Bioinformatics and holobiota | Scoop.it

The MyNewGut Project, (Microbiome's influence on energy balance and brain development/function put into action to tackle diet-related diseases and behaviour) which receives funding from the European Union’s Seventh Framework Programme, will research how the human gut microbiota and its genome (microbiome) influence obesity, behavioural- and lifestyle-related disorders and vice versa. It also aims to identify specific dietary strategies to improve the long-term health of the population.

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2014-2019 European project on microbiota vs. lifestyle, diet, environment

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Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics | Bioinformatics and holobiota | Scoop.it

This is an example of the ‘Anna Karenina principle (AKP)’ applied to microbial communities: disturbed states having many more configurations than undisturbed. We verify this by showing that in a study of inflammatory bowel disease (IBD) phenotypes, ileal Crohn's disease (ICD) is associated with a more variable community.

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US Centers of Prevention Report on Antibiotic Resistance 2013

Alexander Tyakht's insight:

nicely put together facts on drug resistance

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