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Strain/species identification in metagenomes using genome-specific markers

Strain/species identification in metagenomes using genome-specific markers | Bioinformatics and holobiota | Scoop.it

 Application of GSMs identified 45 and 74 microbial strains/species significantly associated with type 2 diabetes patients and obese/lean individuals from corresponding gastrointestinal tract metagenomes, respectively. Our result agreed with previous studies but provided strain-level information. The approach can be directly applied to identify microbial strains/species from raw metagenomes, without the effort of complex data pre-processing.

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Yet another approach at k-mer analysis of human metagenome

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Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013

A conference entitled ‘Human microbiome science: Vision for the future’ was organized in Bethesda, MD from July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and aimed at providing a comprehensive overview of the state of microbiome research, but more importantly to identify and discuss gaps, challenges and opportunities in this nascent field. This report summarizes the presentations but also describes what is needed for human microbiome research to move forward and deliver medical translational applications.

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contains a brief overview of US microbiota trends + should check out the proceedins afterwards

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Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue: PCB

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue: PCB | Bioinformatics and holobiota | Scoop.it

we present the bioinformatics pipeline MEDUSA that facilitates analysis of metagenomic reads at the gene and taxonomic level. We also constructed a global human gut microbial gene catalogue by combining data from 4 studies spanning 3 continents. Using MEDUSA we mapped 782 gut metagenomes to the global gene catalogue and a catalogue of sequenced microbial species.

Alexander Tyakht's insight:

huge meta-combination of gene catalogs from large studies + pipeline for it

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

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes : Nature Biotechnology | Bioinformatics and holobiota | Scoop.it
Sequencing the microbial species present in complex metagenomic samples is made easier with a method that groups genes by co-abundance.
Alexander Tyakht's insight:

Metahit+EMBL+others report on CAGs = MLGs = quasigenomes from correlating groups of genes. The catalog they use is a newer BGI (3.8 mln genes) but less than a just published 9 mln catalog. There are interesting examples in th article on particular bacteria , mobile islands etc.

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BMC Genomics | Full text | Metatranscriptome analysis of fungal strains Penicillium camemberti and Geotrichum candidum reveal cheese matrix breakdown and potential development of sensory properties...

Camembert-type cheese ripening is driven mainly by fungal microflora including Geotrichum candidum and Penicillium camemberti. These species are major contributors to the texture and flavour of typical bloomy rind cheeses. Biochemical studies showed that G. candidum reduces bitterness, enhances sulphur flavors through amino acid catabolism and has an impact on rind texture, firmness and thickness, while P. camemberti is responsible for the white and bloomy aspect of the rind, and produces enzymes involved in proteolysis and lipolysis activities. However, very little is known about the genetic determinants that code for these activities and their expression profile over time during the ripening process.
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SAY CHEEEESE!

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Review: The dynamic microbiome. [FEBS Lett. 2014]

This review will highlight ... temporal variability of the microbiome ... Given the importance of computational methods in the field, this review will also discuss issues and pitfalls in the analysis of microbiome time-series data, and explore several promising new directions for mathematical model and algorithm development.

Alexander Tyakht's insight:

A few basic points to check out before designing the experiment and analyzing metagenomic time series 

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Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution | Bioinformatics and holobiota | Scoop.it

Here, we introduce a novel computational framework, integrating variation in gene abundances across multiple samples with taxonomic abundance data to deconvolve metagenomic samples into taxa-specific gene profiles and to reconstruct the genomic content of community members. This assembly-free method is not bounded by various factors limiting previously described methods of metagenomic binning or metagenomic assembly and represents a fundamentally different approach to metagenomic-based genome reconstruction.

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New! The HMP DACC Releases Expansive Collection of Data

New! The HMP DACC Releases Expansive Collection of Data | Bioinformatics and holobiota | Scoop.it

In April 2014, the HMP Data Analysis and Coordinatin Center (DACC) released a large amount of new sequence data from the HMP sequencing centers and the demonstration projects. This new release, in addition to previously released data, brings the total sequence data stored by the DACC to over 14 terabytes. This expansive set of data will be useful to a large global community of researchers interested in microbes that are associated with both healthy humans and those suffering from numerous conditions and diseases.

Alexander Tyakht's insight:

A ton of data, let's analyze

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Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization (Genome Res)

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization (Genome Res) | Bioinformatics and holobiota | Scoop.it

We developed new metagenomic methods and utilized them to track species and strain level variations in microbial communities in 11 fecal samples collected from a premature infant during the first month of life. Ninety six percent of the sequencing reads were assembled into scaffolds of >500 bp in length that could be assigned to organisms at the strain level. Six essentially complete (∼99%) and two near-complete genomes were assembled for bacteria that comprised as little as 1% of the community, as well as nine partial genomes of bacteria representing as little as 0.05%. In addition, three viral genomes were assembled and assigned to their hosts. 

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interesting ESOM for metagenomic viz

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Placenta Harbors Bacteria, May Impact Fetal Health

Placenta Harbors Bacteria, May Impact Fetal Health | Bioinformatics and holobiota | Scoop.it

Researchers have discovered a small community of bacteria living in a most unlikely place: the placenta, the organ that nourishes a developing fetus through the umbilical cord. The finding overturns the conventional wisdom that the placenta is sterile. The study also suggests that these microbes may come from the mouth, affirming that good oral hygiene may be important for a healthy pregnancy.

 

Aticle http://stm.sciencemag.org/content/6/237/237ra65.abstract

 

Alexander Tyakht's insight:

Interesting news for obstetricians and gynecologists. Do humans exist in a microbial continuum from generation to generation even inside mom's womb?

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Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease - Gastroenterology

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The mutual relationship between the intestinal microbiota and its mammalian host is influenced by diet. Consumption of various nutrients affects the structure of the microbial community and provides substrates for microbial metabolism. The microbiota can produce small molecules that are absorbed by the host and affect many important physiological processes. Age-dependent and societal differences in the intestinal microbiota could result from differences in diet. Examples include differences in the intestinal microbiota of breastfed vs formula-fed infants or differences in microbial richness in people who consume an agrarian plant-based vs a Western diet, which is high in meat and fat. We review how diet affects the structure and metabolome of the human intestinal microbiome and may contribute to health or the pathogenesis of disorders such as coronary vascular disease and inflammatory bowel disease.

 
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Third International Symposium on Human Gut Microbiota in Health and Disease in Mexico City - Gut Microbiota For Health

Third International Symposium on Human Gut Microbiota in Health and Disease in Mexico City - Gut Microbiota For Health | Bioinformatics and holobiota | Scoop.it
For the third consecutive year the “International Symposium of Human Gut Microbiota in Health and Disease” will take place in Mexico City (May 23th and 24th). This meeting is endorsed by the National Institute of Medical Sciences and Nutrition, The Mexican Gastroenterology Association, The Mexican Association of Nutrition, and The Mexican College of Nutritionists, with the support of Danone Institute.
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Microbiome | Abstract | Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. In each case the underlying data are similar and are composed of counts of sequencing reads mapped to a large number of features in each sample

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Data from an in vitro selective growth experiment, an RNA-seq experiment and the Human Microbiome Project 16S rRNA gene abundance dataset were examined by ALDEx2, a compositional data analysis tool that uses Bayesian methods to infer technical and statistical error.

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Gut microbiome of the Hadza hunter-gatherers : Nature Communications

Gut microbiome of the Hadza hunter-gatherers : Nature Communications | Bioinformatics and holobiota | Scoop.it

To explore variation in gut microbiota and to understand how these bacteria may have co-evolved with humans, here we investigate the phylogenetic diversity and metabolite production of the gut microbiota from a community of human hunter-gatherers, the Hadza of Tanzania. We show that the Hadza have higher levels of microbial richness and biodiversity than Italian urban controls. 

Alexander Tyakht's insight:

Surprisingly, they lack Bifidobacteria. It seems to be another research group on Hadza microbiome than http://www.sciencemag.org/content/343/6168/241.full

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BMC Bioinformatics | Full text | Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances in sequencing technologies, new challenges arise for existing bioinformatic tools dedicated to viral metagenome (i.e. virome) analysis as (i) the number of viromes is rapidly growing and (ii) large genomic fragments can now be obtained by assembling the huge amount of sequence data generated for each metagenome.
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Tipping elements in the human intestinal ecosystem : Nature Communications

Tipping elements in the human intestinal ecosystem : Nature Communications | Bioinformatics and holobiota | Scoop.it

we have limited understanding of the mechanisms that control this complex ecosystem. Here, based on a deep phylogenetic analysis of the intestinal microbiota in a thousand western adults, we identify groups of bacteria that exhibit robust bistable abundance distributions. These bacteria are either abundant or nearly absent in most individuals, and exhibit decreased temporal stability at the intermediate abundance range. The abundances of these bimodally distributed bacteria vary independently, and their abundance distributions are not affected by short-term dietary interventions. However, their contrasting alternative states are associated with host factors such as ageing and overweight. We propose that the bistable groups reflect tipping elements of the intestinal microbiota, whose critical transitions may have profound health implications and diagnostic potential.

  
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A new article on ecological modeling of microbiota from our friend Leo 

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UPDATED BGI catalog! An integrated catalog of reference genes in the human gut microbiome

Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. From this we established the integrated gene catalog (IGC) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.

Alexander Tyakht's insight:

got to update our pipelines

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DNA-dependent RNA polymerase detects hidden giant viruses in published databanks

Environmental metagenomic studies show that there is a “dark matter”, composed of sequences not linked to any known organism, as determined mainly using ribosomal DNA sequences, which therefore ignore giant viruses. DNA-dependent RNA polymerase (RNAP) genes are universal in microbes and conserved in giant viruses, and may replace rDNA for identifying microbes. ... To explore the dark matter, we used viral RNAP2 and reconstructed putative ancestral RNAP2, which were significantly superior in detecting distant clades than current sequences, and we revealed two additional unknown mimiviruses, misclassified as an euryarchaeote and a oomycete plant pathogen, and detected unknown putative viral clades. 

Alexander Tyakht's insight:

Giant viruses as a component of metagenomic dark matter 

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Access : Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men : The ISME Journal

Here we report a comprehensive and deep microbiota analysis of 14 obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSPs) and a weight-loss (WL) diet. We analyzed the composition, diversity and dynamics of the fecal microbiota on each dietary regime by phylogenetic microarray and quantitative PCR (qPCR) analysis. In addition, we analyzed fecal short chain fatty acids (SCFAs) as a proxy of colonic fermentation, and indices of insulin sensitivity from blood samples. The diet explained around 10% of the total variance in microbiota composition, which was substantially less than the inter-individual variance. Yet, each of the study diets induced clear and distinct changes in the microbiota. 

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publication by group of W. de Vos 

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ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq

ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq | Bioinformatics and holobiota | Scoop.it

 We show that the partitioning of within-condition to between-condition variation cannot reasonably be ignored, whether in single-organism RNA-Seq or in Meta-RNA-Seq experiments, and further find that commonly-used RNA-Seq analysis tools, as described in the literature, do not enforce the constraint that the sum of relative expression levels must be one, and thus report expression levels that are systematically distorted. These two factors lead to misleading inferences if not properly accommodated. As it is usually only the biological between-condition and within-condition differences that are of interest, we developed ALDEx, an ANOVA-like differential expression procedure, to identify genes with greater between- to within-condition differences. 

Alexander Tyakht's insight:

stat method for differential metatranscriptomics

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The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts | Bioinformatics and holobiota | Scoop.it

By mapping their reads to 1,751 reference genome sequences and analyzing the resulting relative strain abundance in each sample we present metrics and visualizations that can help identify strains of interest for experimentalists. We also show that approximately 14 strains of 10 species account for 80% of the mapped reads from a typical stool sample, indicating that the function of a community may not be irreducibly complex. Some of these strains account for >20% of the sequence reads in a subset of samples but are absent in others, a dichotomy that could underlie biological differences among subjects. These data should serve as an important strain selection resource for the community of researchers who take experimental approaches to studying the human microbiota.

Alexander Tyakht's insight:

some notes about 16S vs WGS, highly variable "strains" an preferential mapping to ref

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Dynamics and associations of microbial community types across the human body : Nature

Dynamics and associations of microbial community types across the human body : Nature | Bioinformatics and holobiota | Scoop.it

Using additional data collected over the course of 12–18 months, we used Dirichlet multinomial mixture models4 to partition the data into community types for each body site and made three important observations. First, there were strong associations between whether individuals had been breastfed as an infant, their gender, and their level of education with their community types at several body sites. Second, although the specific taxonomic compositions of the oral and gut microbiomes were different, the community types observed at these sites were predictive of each other. Finally, over the course of the sampling period, the community types from sites within the oral cavity were the least stable, whereas those in the vagina and gut were the most stable. 


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Case-Based Introduction to Biostatistics

Case-Based Introduction to Biostatistics | Bioinformatics and holobiota | Scoop.it

The course objective is to enable each student to enhance his or her quantitative scientific reasoning about problems related to human health.

Alexander Tyakht's insight:

must join

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OpenBiome

Alexander Tyakht's insight:

We founded OpenBiome, a nonprofit 501(c)(3) organization, after watching a friend and family member suffer through 18 months of C. difficile and 7 rounds of vancomycin before finally receiving a successful, life-changingFecal Microbiota Transplantation (FMT). The remarkable efficacy of this treatment and the great lengths required to receive it convinced us that we needed to help expand access. After many discussions with local clinicians and the FDA, we launched OpenBiome in 2012 to make FMT faster and easier for patients and doctors alike.

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Visualising Data

Visualising Data | Bioinformatics and holobiota | Scoop.it
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Workshops on data viz + blog

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Towards predictive models of the human gut microbiome

Towards predictive models of the human gut microbiome | Bioinformatics and holobiota | Scoop.it

Via Dmitry Alexeev
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Dmitry Alexeev's curator insight, April 18, 4:31 AM

fine review of modelling and way to go directions