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Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission | Bioinformatics and holobiota | Scoop.it

Here, we surveyed the gut microbiome of the T-bet−/− Rag2−/− mouse model of colitis during active disease and treatment-induced remission. Microbial features modified among these conditions included altered potential for carbohydrate and energy metabolism and bacterial pathogenesis, specifically cell motility and signal transduction pathways. We also observed an increased capacity for xenobiotics metabolism, including benzoate degradation, a pathway linking host adrenergic stress with enhanced bacterial virulence, and found decreased levels of fecal dopamine in active colitis. When transferred to gnotobiotic mice, gut microbiomes from mice with active disease versus treatment-induced remission elicited varying degrees of colitis. Thus, our study provides insight into specific microbial clades and pathways associated with health, active disease and treatment interventions in a mouse model of colitis.

Alexander Tyakht's insight:

Nice example of experimental mice model: IBD, knockouts, antibiotics, FMT. Data analysis is standard and performed using Lefse and other tools of Huttenhower lab.

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Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data | Bioinformatics and holobiota | Scoop.it
PLOS Computational Biology is an open-access

Via Dmitry Alexeev
Alexander Tyakht's insight:

genomic diversity with focus on pathogen populations

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Dmitry Alexeev's curator insight, April 1, 1:49 AM

stream of knowledge lately has been working to keep us thinking tight

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New York Times: Say Hello to the 100 Trillion Bacteria That Make Up Your Microbiome

New York Times: Say Hello to the 100 Trillion Bacteria That Make Up Your Microbiome | Bioinformatics and holobiota | Scoop.it
Medicine used to be obsessed with eradicating the tiny bugs that live within us. Now we’re beginning to understand all the ways they keep us healthy.
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Programmable bacteria detect and record an environmental signal in the mammalian gut (PNAS)

We constructed engineered bacteria that survive in the mammalian gut and sense, remember, and report on their experiences. 

Alexander Tyakht's insight:

A lot of bioengineering details but to put simply : E. coli with a antibiotic-sensing switch in a phague are fed to mice, "switch" after AB treatment and preserve it on exiting the host.

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Application of zero-inflated negative binomial mixed model to human microbiota sequence data

https://peerj.com/preprints/215v1.pdf

Alexander Tyakht's insight:

metagenomic statistics explained

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DNA microarray analysis reveals that antibiotic resistance-gene diversity in human gut microbiota is age related : Scientific Reports : Nature Publishing Group

DNA microarray analysis reveals that antibiotic resistance-gene diversity in human gut microbiota is age related : Scientific Reports : Nature Publishing Group | Bioinformatics and holobiota | Scoop.it

The human gut is a reservoir for antibiotic resistance genes. In this report, we used a DNA microarray chip covering 369 resistance types to investigate the relationship between antibiotic resistance-gene diversity and human age. 

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Classification and quantification of bacteriophage taxa in human gut metagenomes : The ISME Journal

Bacteriophages have key roles in microbial communities, to a large extent shaping the taxonomic and functional composition of the microbiome, but data on the connections between phage diversity and the composition of communities are scarce. Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. On average, five phage taxa were identified in each sample, with up to three of these being highly abundant. The abundances of most phage taxa vary by up to four orders of magnitude between the samples, and several taxa that are highly abundant in some samples are absent in others. Significant correlations exist between the abundances of some phage taxa and human host metadata: for example, ‘Group 936 lactococcal phages’ are more prevalent and abundant in Danish samples than in samples from Spain or the United States of America. Quantification of phages that exist as integrated prophages revealed that the abundance profiles of prophages are highly individual-specific and remain unique to an individual over a 1-year time period, and prediction of prophage lysis across the samples identified hundreds of prophages that are apparently active in the gut and vary across the samples, in terms of presence and lytic state. Finally, a prophage–host network of the human gut was established and includes numerous novel host–phage associations.

Alexander Tyakht's insight:

interesting metagenomic project from EMBL et al

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Jeffrey Gordon | TEDxGatewayArch

Jeffrey Gordon | TEDxGatewayArch | Bioinformatics and holobiota | Scoop.it

Jeffrey Gordon is the founding Director of Washington University’s Center for Genome Sciences and Systems Biology. His lab studies how the trillions of microbes living in our gut impact healthy growth during infancy, how their activities shape the nutritional value of the foods we eat, and what roles they play in under nutrition and obesity. He is a member of the National Academy of Sciences.

 

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"We never die alone... we have trillions of friends" A story about kwashiorkor (malnutrition) and microbiota in Malawi.

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A solid quality-control analysis of AB SOLiD short-read sequencing data

...We focus here on the two-base color code chemistry of AB SOLiD sequencers and propose a comprehensive quality control methodological and software pipeline. We used existing and custom tools to detect and purge short-reads of some common flaws due to sequencing errors and chemical hitches. We apply them to a cohort of SOLiD 4 runs and measure their joint efficacy in terms of the resulting ability to detect the greatest possible number of true variants.

Alexander Tyakht's insight:

One of the few articles examining our central seq tool

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Characteristics of the Gut Microbiota in Obese Children with Allergic Diseases | Open Access | OMICS Publishing Group

Characteristics of the Gut Microbiota in Obese Children with Allergic Diseases | Open Access | OMICS Publishing Group | Bioinformatics and holobiota | Scoop.it

There are many evidences, that obesity increases the risk of asthma and atopic diseases. Therefore, misbalance in the gut microbiota is considered one of the micro ecological factors responsible for the increase of body mass and changes in energy metabolism. The aim of study was to investigate the characteristics of children gut microbiota, and to recognize relations with obesity, as well as allergic disorders. 

Alexander Tyakht's insight:

Our neighbours (Sechenov Academy @ Bolshaya Pirogovskaya, Moscow) take an culture-based approach towards gut microbiota. We could collaborate and do a 16S rRNA for their interesting cohort.

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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.

Alexander Tyakht's insight:

Yet another approach at k-mer analysis of human metagenome

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The symbiotic intestinal ciliates and the evolution of their hosts

An extensive study on excrement and rumen fluids in plant-eating mammals from all over the whole world shows that the ciliates in their guts have evolved in parallel with them.

Alexander Tyakht's insight:

gut protists

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"Gut Microbiota for Health"

"Gut Microbiota for Health" | Bioinformatics and holobiota | Scoop.it

The place for scientific debate

Alexander Tyakht's insight:

interesting aggregator of m-biota news

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Journal of Physiological Anthropology | Abstract | Fermented foods, microbiota, and mental health: ancient practice meets nutritional psychiatry

The purposeful application of fermentation in food and beverage preparation, as a means to provide palatability, nutritional value, preservative, and medicinal properties, is an ancient practice.
Alexander Tyakht's insight:

A multi-referenced review on link between food-fermenting bacteria and human health.

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Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible | Bioinformatics and holobiota | Scoop.it

Current practice in the normalization of microbiome count data is inefficient in the statistical sense.

Alexander Tyakht's insight:

Must check for metagemers - statistical approach similar to RNA-seq edgeR (negative binomial distribution) is more fair than simply equalizing the number of reads per each sequenced library 

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Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota (ISMEJ)

In this study, we illustrated a model of this mucosa bacterial communities’ biogeography, based on the largest data set so far, obtained via 454-pyrosequencing of bacterial 16S rDNAs associated with 77 matched biopsy tissue samples taken from terminal ileum, ileocecal valve, ascending colon, transverse colon, descending colon, sigmoid colon and rectum of 11 healthy adult subjects.

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Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries using Sparse Linear Regression

http://arxiv.org/pdf/1402.0511.pdf

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CULTURED COLLECTION OF GUT MICROBIAL COMMUNITY - Gordon, Jeffrey I.

The present invention encompasses cultured collections of a gut microbial community, models comprising such cultures, and methods of use thereof.
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The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease | Bioinformatics and holobiota | Scoop.it

Inflammatory bowel diseases (IBDs), including Crohn’s disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.

Alexander Tyakht's insight:

A lot of data: >1300 16S rRNA + 43 whole genome metagenomes

Interestingly, stool samples between cases and controls vary much less than mucosal.

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Statistics: Biomedicine must look beyond P values : Nature : Nature Publishing Group

Statistics: Biomedicine must look beyond P values : Nature : Nature Publishing Group | Bioinformatics and holobiota | Scoop.it

"The P value was never meant to be used the way it's used today."

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Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium

Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium | Bioinformatics and holobiota | Scoop.it

In 1996, the exploration of an archeological Middle Ages site in Namur, Belgium yielded a closed barrel, such as those commonly used at that time as pits or latrines. The barrel was located at a depth of 3.80 m beneath the modern soil level and contained a 121.4 g, dark-brown, well preserved coprolite specimen.

Alexander Tyakht's insight:

New coprolite metagenomics

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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
Alexander Tyakht's insight:

Free book - overview of modern bioinformatics

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Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission | Bioinformatics and holobiota | Scoop.it

Here, we surveyed the gut microbiome of the T-bet−/− Rag2−/− mouse model of colitis during active disease and treatment-induced remission. Microbial features modified among these conditions included altered potential for carbohydrate and energy metabolism and bacterial pathogenesis, specifically cell motility and signal transduction pathways. We also observed an increased capacity for xenobiotics metabolism, including benzoate degradation, a pathway linking host adrenergic stress with enhanced bacterial virulence, and found decreased levels of fecal dopamine in active colitis. When transferred to gnotobiotic mice, gut microbiomes from mice with active disease versus treatment-induced remission elicited varying degrees of colitis. Thus, our study provides insight into specific microbial clades and pathways associated with health, active disease and treatment interventions in a mouse model of colitis.

Alexander Tyakht's insight:

Nice example of experimental mice model: IBD, knockouts, antibiotics, FMT. Data analysis is standard and performed using Lefse and other tools of Huttenhower lab.

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2013 Visualization Challenge

2013 Visualization Challenge | Bioinformatics and holobiota | Scoop.it

Science and the National Science Foundation present the winners of the 2013 International Science and Engineering Visualization Challenge.

  
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nice sci-visualisations

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What is a ‘Healthy’ Microbiome? — NOVA Next | PBS

What is a ‘Healthy’ Microbiome? — NOVA Next | PBS | Bioinformatics and holobiota | Scoop.it

In psychology and other social sciences, the participants in most experiments are college students from so-called WEIRD countries—that is, Western, educated, industrialized, rich, and democratic. Such nations include just 12% of the world’s population, and the behaviour of their students—an even narrower stratum—is distinctly unrepresentative of humanity at large.

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On Amazonian hunter-gatherers as potential healthy microbiota carriers, unrepresentativeness of existing global metagenomic datasets and more 

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A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system | Bioinformatics and holobiota | Scoop.it

Here we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing PMI to be estimated within approximately 3 days over 48 days. Our results provide a detailed understanding of bacterial and microbial eukaryotic ecology within a decomposing corpse system and suggest that microbial community data can be developed into a forensic tool for estimating PMI. - See more at: http://elife.elifesciences.org/content/2/e01104#sthash.xhnJj2WV.dpuf

Alexander Tyakht's insight:

Нет, весь я не умру — душа в заветной лире
Мой прах переживет и тленья убежит

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