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

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Thesis - E. coli adaptation to the extraintestinal niche: using natural variation to explore mechanisms of pathogenesis

Thesis - E. coli adaptation to the extraintestinal niche: using natural variation to explore mechanisms of pathogenesis | Bioinformatics and holobiota | Scoop.it

Part 2 (chapters 4-5) explores the evolution and diversification of an E. coli strain over the course of a long-term chronic infection, in this case in the airways of an individual with cystic fibrosis (CF). Patients with CF develop chronic lung infections that are frequently polymicrobial. Work by our collaborators demonstrated that E. coli can not only colonize the lungs of cystic fibrosis patients, it can persist for months to years and undergoes characteristic phenotypic changes (mucoidy, small colony variants, and antibiotic-resistance) seen in typical CF pathogens during chronic infection. We sequenced the genomes of clonal isolates with varying phenotypes from a single patient and identified mutations specific to each. These mutations allowed us to distinguish and follow lineages that arose over the course of infection, and one mutation, a truncation in mdoH, was definitively shown to be the cause of the mucoid phenotype.

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coming in 2016

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Collective unconscious: how gut microbes shape human behavior

Collective unconscious: how gut microbes shape human behavior | Bioinformatics and holobiota | Scoop.it

Via Dmitry Alexeev
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Dmitry Alexeev's curator insight, March 10, 12:33 PM

root of uncosciousness

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Simultaneous observation of the quantization and the interference pattern of a plasmonic near-field : Nature Communications : Nature Publishing Group

Simultaneous observation of the quantization and the interference pattern of a plasmonic near-field : Nature Communications : Nature Publishing Group | Bioinformatics and holobiota | Scoop.it
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Light captured as particle and wave at the same time!

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Home : Statistics for Biologists

Home : Statistics for Biologists | Bioinformatics and holobiota | Scoop.it
A collection of articles from the publisher of Nature that discusses statistical issues biologists should be aware of and provides practical advice to improve the statistical rigor and reproducibility of their work.
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Combating Antibiotic Resistance in COPD Patients | Annals of Long Term Care

Combating Antibiotic Resistance in COPD Patients | Annals of Long Term Care | Bioinformatics and holobiota | Scoop.it

On January 9, 2014, the investigators announced that they had received a $2.3 million grant from the National Institute of Allergy and Infectious Diseases to fund a new project under an ongoing study on the pathogenesis of H influenzae, which has spanned nearly three decades. For the next 5 years, the team will be studying how H influenzae is able to survive in the body from months to years in the airways of COPD patients and resist repeated courses of antibiotics. With the ultimate goal of developing new, more effective vaccines for preventing and treating infections in COPD patients, the investigators will evaluate potential vaccine antigens currently under development.

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ar IN copd

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The first 1000 cultured species of the human gastrointestinal microbiota

The first 1000 cultured species of the human gastrointestinal microbiota | Bioinformatics and holobiota | Scoop.it

This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years.

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tips for reports

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Where Next for Microbiome Research?

The last decade has seen a staggering transformation in our knowledge of microbial communities. Here, seven short pieces speculate as to what the next ten years might hold in store.
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perspective from opinion-leaders

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Cell: Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

Cell: Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease | Bioinformatics and holobiota | Scoop.it

Highlights
• The enteric virome is abnormal in multiple inflammatory bowel disease patient cohorts
• The enteric virome richness increases in Crohn’s disease and ulcerative colitis
• Decreases in bacterial diversity and richness in IBD do not explain virome changes
• Virome changes in Crohn’s disease and ulcerative colitis are disease specific

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Free bacterial virions analysis show UC and CD samples  are enriched in Caudovirales bacteriophages

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thesis: "Mechanisms of bacterial uncultivability in the human gut microbiome" by Kathrin Fenn

One organism obtained from a fecal sample was closely related to Faecalibacterium prausnitzii, an important commensal of the human gut flora, which may be connected to intestinal health. Growth of this isolate and its cultivable relative was enhanced by Escherichia coli, which was found to be a common helper for uncultured bacteria. In order to identify the growth factor, an E. coli deletion library was screened and a mutant lacking menaquinone biosynthesis was found to be impaired in its ability to induce the growth of Faecalibacterium. Genome analysis indicated that Faecalibacteria depend on menaquinone for anaerobic fumarate respiration. The growth of several other isolates was induced by menaquinone, suggesting that menaquinone-dependence can be found among gut bacteria from various phyla.
The second part of the study focused on potential host-produced growth factors. A bacterium closely related to Akkermansia muciniphila initially appeared to be dependent on mucin but the isolate had the ability to grow on glucose after a long lag phase. Domestication through subcultivation on glucose occurred quickly in all cells and shortened this lag phase. Genome analysis revealed no missing pathways compared to the cultivable relative and together with the frequency of domestication it could be hypothesized that a change in gene expression leading to a shift in metabolism occurred during domestication. It is often observed that previously uncultured bacteria gain the ability to grow readily in the laboratory after a few passages. This led to a new hypothesis that the inability to adapt the metabolism quickly may be the underlying mechanism of uncultivability in many bacteria.

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The microbiome mutiny hypothesis: can our microbiome turn against us when we are old or seriously ill?

The symbiotic organisms of the healthy microbiome tend to be harmless or even beneficial for the host; however, some symbionts are able to adjust their virulence in response to external stimuli. Evolutionary theory suggests that optimal virulence might increase if the mortality of the host (from unrelated causes) increases.
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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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Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria

Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria | Bioinformatics and holobiota | Scoop.it

Anaerobic microbial choline metabolism, a disease-associated metabolic pathway, exemplifies this challenge, as the specific human gut microorganisms responsible for this transformation have not yet been clearly identified. In this study, we established the link between a bacterial gene cluster, the choline utilization (cut) cluster, and anaerobic choline metabolism in human gut isolates by combining transcriptional, biochemical, bioinformatic, and cultivation-based approaches. Quantitative reverse transcription-PCR analysis andin vitro biochemical characterization of two cut gene products linked the entire cluster to growth on choline and supported a model for this pathway. Analyses of sequenced bacterial genomes revealed that the cut cluster is present in many human gut bacteria, is predictive of choline utilization in sequenced isolates, and is widely but discontinuously distributed across multiple bacterial phyla.

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Temporal and technical variability of human gut metagenomes

We performed metagenomic analysis on fecal samples from seven subjects collected over a period of up to two years to investigate temporal variability and assess preservation-induced variation, specifically, fresh frozen compared to RNALater. We also monitored short-term disturbances caused by antibiotic treatment and bowel cleansing in one subject.

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Sewage Reflects the Microbiomes of Human Populations

Sewage Reflects the Microbiomes of Human Populations | Bioinformatics and holobiota | Scoop.it

We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage.

 

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The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, orLachnospiraceae/Ruminococcaceae. 

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enterotypes of sewage are the same as upstairs

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UPARSE: highly accurate OTU sequences from microbial amplicon reads : Nature Methods : Nature Publishing Group

To determine microbial community structure, the UPARSE software extracts operational taxonomic unit (OTU) representative sequences with high accuracy on the basis of amplified marker-gene sequences.
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Power failure: why small sample size undermines the reliability of neuroscience : Article : Nature Reviews Neuroscience

Power failure: why small sample size undermines the reliability of neuroscience : Article : Nature Reviews Neuroscience | Bioinformatics and holobiota | Scoop.it
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Cell - Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

•The enteric virome is abnormal in multiple inflammatory bowel disease patient cohorts•The enteric virome richness increases in Crohn’s disease and ulcerative colitis•Decreases in bacterial diversity and richness in IBD do not explain virome changes•Virome changes in Crohn’s disease and ulcerative colitis are disease specific
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lots of phages in IBD - this fact has been around for a while however

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Mongolians core gut microbiota and its correlation with seasonal dietary changes : Scientific Reports : Nature Publishing Group

Mongolians core gut microbiota and its correlation with seasonal dietary changes : Scientific Reports : Nature Publishing Group | Bioinformatics and holobiota | Scoop.it
Historically, the Mongol Empire ranks among the world's largest contiguous empires, and the Mongolians developed their unique lifestyle and diet over thousands of years. In this study, the intestinal microbiota of Mongolians residing in Ulan Bator, TUW province and the Khentii pasturing area were studied using 454 pyrosequencing and q-PCR technology. We explored the impacts of lifestyle and seasonal dietary changes on the Mongolians' gut microbes. At the phylum level, the Mongolians's gut populations were marked by a dominance of Bacteroidetes (55.56%) and a low Firmicutes to Bacteroidetes ratio (0.71). Analysis based on the operational taxonomic unit (OTU) level revealed that the Mongolian core intestinal microbiota comprised the genera Prevotella, Bacteroides, Faecalibacterium, Ruminococcus, Subdoligranulum and Coprococcus. Urbanisation and life-style may have modified the compositions of the gut microbiota of Mongolians from Ulan Bator, TUW and Khentii. Based on a food frequency questionnaire, we found that the dietary structure was diverse and stable throughout the year in Ulan Bator and TUW, but was simple and varied during the year in Khentii. Accordingly, seasonal effects on intestinal microbiota were more distinct in Khentii residents than in TUW or Ulan Bator residents.
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rural microbiota changes with seasonary diet, while urban does not

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A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes

We propose a two-stage statistical procedure for selecting informative features and identifying differentially abundant features between two or more groups of microbial communities. In the functional analysis of metagenomes, the features may refer to the pathways, subsystems, functional roles and so on. In the first stage of the proposed procedure, the informative features are selected using elastic net as reducing the dimension of metagenomic data. In the second stage, the differentially abundant features are detected using generalized linear models with a negative binomial distribution. Compared with other available methods, the proposed approach demonstrates better performance for most of the comprehensive simulation studies. The new method is also applied to two real metagenomic datasets related to human health. Our findings are consistent with those in previous reports.

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How informative is the mouse for human gut microbiota research?

Mouse models allow perturbations in gut microbiota to be studied in a controlled experimental setup, and thus help in assessing causality of the complex host-microbiota interactions and in developing mechanistic hypotheses. However, pitfalls should be considered when translating gut microbiome research results from mouse models to humans. In this Special Article, we discuss the intrinsic similarities and differences that exist between the two systems, and compare the human and murine core gut microbiota based on a meta-analysis of currently available datasets. Finally, we discuss the external factors that influence the capability of mouse models to recapitulate the gut microbiota shifts associated with human diseases, and investigate which alternative model systems exist for gut microbiota research.

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when it comes to human microbiota, mice might not be the best choice for model animal 

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Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data | Bioinformatics and holobiota | Scoop.it

We undertook a broad analysis of butyrate-producing pathways and individual genes by screening 3,184 sequenced bacterial genomes from the Integrated Microbial Genome database. Genomes of 225 bacteria with a potential to produce butyrate were identified, including many previously unknown candidates. The majority of candidates belong to distinct families within the Firmicutes, but members of nine other phyla, especially fromActinobacteria, Bacteroidetes, Fusobacteria, Proteobacteria, Spirochaetes, andThermotogae, were also identified as potential butyrate producers. The established gene catalogue (3,055 entries) was used to screen for butyrate synthesis pathways in 15 metagenomes derived from stool samples of healthy individuals provided by the HMP (Human Microbiome Project) consortium.

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enteric currency sources

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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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