Bioinformatics and holobiota
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Элементы - новости науки: Новые результаты долгосрочного эволюционного эксперимента: приспособленность подопытных бактерий продолжает расти

Элементы - новости науки: Новые результаты долгосрочного эволюционного эксперимента: приспособленность подопытных бактерий продолжает расти | Bioinformatics and holobiota | Scoop.it

Experimental studies of evolution have increased greatly in number in recent years, stimulated by the growing power of genomic tools. However, organismal fitness remains the ultimate metric for interpreting these experiments, and the dynamics of fitness remain poorly understood over long time scales. Here, we examine fitness trajectories for 12 Escherichia coli populations during 50,000 generations. Mean fitness appears to increase without bound, consistent with a power law. We also derive this power-law relation theoretically by incorporating clonal interference and diminishing-returns epistasis into a dynamical model of changes in mean fitness over time.

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famous Lenski experiment still going on

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An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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DBH: A de Bruijn graph-based heuristic method for clustering large-scale 16S rRNA sequences into OTUs

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Frontiers | The hologenome across environments and the implications of a host-associated microbial repertoire | Microbiology

Frontiers | The hologenome across environments and the implications of a host-associated microbial repertoire | Microbiology | Bioinformatics and holobiota | Scoop.it
Our understanding of the diverse interactions between hosts and microbes has grown profoundly over the past two decades and, as a product, has revolutionized our knowledge of the life sciences. Through primarily laboratory experiments, the current framework for holobionts and their respective hologenomes aims to decipher the underpinnings and implications of symbioses between host and microbiome. However, the laboratory setting restricts the full spectrum of host-associated symbionts as compared to those found in nature; thus, limiting the potential for a holistic interpretation of the functional roles the microbiome plays in host biology. When holobionts are studied in nature, associated microbial communities vary considerably between conditions, resulting in more microbial associates as part of the ‘hologenome’ across environments than in either environment alone. We review and synthesize empirical evidence suggesting that hosts may have the ability to associate with a larger associated microbial network that, in part, corresponds to experiencing diverse environmental conditions. To conceptualize the interactions between host and microbiome in an ecological context, we suggest the ‘host-associated microbial repertoire,’ which is the sum of microbial species a host may associate with over the course of its life-history under all encountered environmental circumstances. Furthermore, using examples from both terrestrial and marine ecosystems, we discuss how this concept may be used as a framework to compare the ability of the holobiont to acclimate and adapt to environmental variation, and propose three ‘signatures’ of the concept.
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Biases in genome reconstruction from metagenomic data

Background: Technological advances in sequencing, assembly and segregation of resulting contigs into species-specific bins has enabled the reconstruction of individual genomes from environmental metagenomic data sets. Though a powerful technique, it is shadowed by an inability to truly determine whether assembly and binning techniques are accurate, specific, and sensitive due to a lack of complete reference genome sequences against which to check the data. Errors in genome reconstruction, such as missing or mis-attributed activities, can have a detrimental effect on downstream metabolic and ecological modeling, and thus it is important to assess the accuracy of the process. Methods: We compared genomes reconstructed from metagenomic data to complete genome sequences of 10 organisms isolated from the same community to identify regions not captured by typical binning techniques. The nucleotide content, as %G+C and tetranucleotide frequencies, and sequence redundancy within both the genome and across the metagenome were determined for both the captured and uncaptured regions. This direct comparison allowed us to evaluate the efficacy of nucleotide composition and coverage profiles as elements of binning protocols and look for biases in sequence characteristics and gene content in regions missing from the reconstructions. Results: We found that repeated sequences were frequently missed in the reconstruction process as were short sequences with variant nucleotide composition. Genes encoded on the missing regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function. Conclusions: Our observation of increased mis-binning of short regions, especially those with variant nucleotide content, and repeated regions implies that factors which affect assembly efficiency also impact binning accuracy. To a large extent, mis-binned regions appear to derive from mobile elements. Our results support genome reconstruction as a robust process, and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function.
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Metabolome of human gut microbiome is predictive of host dysbiosis

Metabolome of human gut microbiome is predictive of host dysbiosis | Bioinformatics and holobiota | Scoop.it
Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome’s interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on its community metabolome; an emergent property of the microbiome. Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles. Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome–host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.
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Community structure follows simple assembly rules in microbial microcosms

Community structure follows simple assembly rules in microbial microcosms | Bioinformatics and holobiota | Scoop.it
Survival of competing microbial species pairs predicts competition outcome between a greater number of species: species that coexist with each other in pairs will survive, species that are excluded by any of the surviving species will go extinct.
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Cospeciation of gut microbiota with hominids

Cospeciation of gut microbiota with hominids | Bioinformatics and holobiota | Scoop.it
The bacteria that make their home in the intestines of modern apes and humans arose from ancient bacteria that colonized the guts of our common ancestors. Moeller et al. have developed a method to compare rapidly evolving gyrB gene sequences in fecal samples from humans and wild chimpanzees, bonobos, and gorillas (see the Perspective by Segre and Salafsky). Comparison of the gyrB phylogenies of major bacterial lineages reveals that they mostly match the apehominid phylogeny, except for some rare symbiont transfers between primate species. Gut bacteria therefore are not simply acquired from the environment, but have coevolved for millions of years with hominids to help shape our immune systems and development.

Science , this issue p. [380][1]; see also p. [350][2]

[1]: /lookup/doi/10.1126/science.aaf3951
[2]: /lookup/doi/10.1126/science.aag2788
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Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients | Bioinformatics and holobiota | Scoop.it
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Inulin and oligofructose in the dietary fibre concept | British Journal of Nutrition | Cambridge Core

Inulin and oligofructose in the dietary fibre concept - Volume 87 Issue S2 - C. Cherbut
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Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions

Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions | Bioinformatics and holobiota | Scoop.it
Dietary modulation of the gut microbiota impacts human health. Here we investigated the hitherto unknown effects of resistant starch type 4 (RS4) enriched diet on gut microbiota composition and short-chain fatty acid (SCFA) concentrations in paralle
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Interconnected microbiomes and resistomes in low-income human habitats : Nature : Nature Research

Interconnected microbiomes and resistomes in low-income human habitats : Nature : Nature Research | Bioinformatics and holobiota | Scoop.it
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Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life | Bioinformatics and holobiota | Scoop.it
Bäckhed et al. assessed the gut microbiomes of 98 Swedish mothers and their infants
during the first year of life. Cessation of breast-feeding was identified as a major
factor in determining gut microbiota maturation, with distinct shifts in signature
species being hallmarks of its functional maturation.
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Patterned progression of bacterial populations in the premature infant gut

Patterned progression of bacterial populations in the premature infant gut | Bioinformatics and holobiota | Scoop.it
It is increasingly apparent that bacteria in the gut are important determinants of health and disease in humans. However, we know remarkably little about how this organ transitions from a sterile/near-sterile state at birth to one that soon harbors
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Mismatch between Probiotic Benefits in Trials versus Food Products

Mismatch between Probiotic Benefits in Trials versus Food Products | Bioinformatics and holobiota | Scoop.it
Probiotic food products contain a variety of different bacterial strains and may offer different health effects. The objective was to document the prevalence and dosage of probiotic strains in the Canadian food supply and to review the literature investigating these strains in order to understand what health benefits these products may offer. The Food Label Information Program was used to identify probiotic-containing products in the food supply. PubMed, Web of Science, and Embase were searched for randomized controlled trials that tested the health effects of these strains in humans. There were six probiotic strains/strain combinations identified in the food supply. Thirty-one studies investigated these strains and found that they are associated with decreased diarrhea and constipation, improved digestive symptoms, glycemic control, antioxidant status, blood lipids, oral health, and infant breastfeeding outcomes, as well as enhanced immunity and support for Helicobacter pylori eradication. There were a limited number of studies investigating these strains. Many studies were funded by the food industry and tested dosages that were up to twenty-five times the dosage found in most food products. Probiotic food products could have health benefits not currently reported on their labels. However, many dosages are too low to provide the benefits demonstrated in clinical trials. Further research is needed to enable more effective use of these functional foods.
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NLRP6 Protects Il10−/− Mice from Colitis by Limiting Colonization of Akkermansia muciniphila

NLRP6 Protects Il10−/− Mice from Colitis by Limiting Colonization of Akkermansia muciniphila | Bioinformatics and holobiota | Scoop.it
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A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome

A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome | Bioinformatics and holobiota | Scoop.it
Background The human microbiota plays a key role in health and disease, and bacteriocins, which are small, bacterially produced, antimicrobial peptides, are likely to have an important function in the stability and dynamics of this community. Here we examined the density and distribution of the subclass I lantibiotic modification protein, LanB, in human oral and stool microbiome datasets using a specially constructed profile Hidden Markov Model (HMM). Methods The model was validated by correctly identifying known lanB genes in the genomes of known bacteriocin producers more effectively than other methods, while being sensitive enough to differentiate between different subclasses of lantibiotic modification proteins. This approach was compared with two existing methods to screen both genomic and metagenomic datasets obtained from the Human Microbiome Project (HMP). Results Of the methods evaluated, the new profile HMM identified the greatest number of putative LanB proteins in the stool and oral metagenome data while BlastP identified the fewest. In addition, the model identified more LanB proteins than a pre-existing Pfam lanthionine dehydratase model. Searching the gastrointestinal tract subset of the HMP reference genome database with the new HMM identified seven putative subclass I lantibiotic producers, including two members of the Coprobacillus genus. Conclusions These findings establish custom profile HMMs as a potentially powerful tool in the search for novel bioactive producers with the power to benefit human health, and reinforce the repertoire of apparent bacteriocin-encoding gene clusters that may have been overlooked by culture-dependent mining efforts to date.
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Frontiers | Evolutionary Biology Needs Wild Microbiomes | Frontiers in Microbiology

Frontiers | Evolutionary Biology Needs Wild Microbiomes | Frontiers in Microbiology | Bioinformatics and holobiota | Scoop.it
The microbiome is a vital component to the evolution of a host and much of what we know about the microbiome derives from studies on humans and captive animals. But captivity alters the microbiome and mammals have unique biological adaptations that affect their microbiomes (e.g., milk). Birds represent over 30% of known tetrapod diversity and possess their own suite of adaptations relevant to the microbiome. In a previous study, we showed that 59 species of bird displayed immense variation in their microbiomes and host (bird) taxonomy and ecology were most correlated with the gut microbiome. In this Frontiers Focused Review, I put those results in a broader context by discussing how collecting and analyzing wild microbiomes contributes to the main goals of evolutionary biology and the specific ways that birds are unique microbial hosts. Finally, I outline some of the methodological considerations for adding microbiome sampling to the research of wild animals and urge researchers to do so. To truly understand the evolution of a host, we need to understand the millions of microorganisms that inhabit it as well: evolutionary biology needs wild microbiomes.
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Gene expression profiling gut microbiota in different races of humans

Gene expression profiling gut microbiota in different races of humans | Bioinformatics and holobiota | Scoop.it
The gut microbiome is shaped and modified by the polymorphisms of microorganisms in the intestinal tract.
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A macroecological theory of microbial biodiversity

A macroecological theory of microbial biodiversity | Bioinformatics and holobiota | Scoop.it
Testing widely known biodiversity models on a dataset of >20,000 microbial community samples from a wide variety of ecosystems, the authors find that microbial abundance and diversity across scales is best predicted by a model of lognormal dynamics.
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An overview of major metagenomic studies on human microbiomes in health and disease

An overview of major metagenomic studies on human microbiomes in health and disease | Bioinformatics and holobiota | Scoop.it
Many microbes are important symbiotes of human. They form specific microbiota communities, participate in various kinds of biological processes of their host and thus deeply affect human health status
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The ISME Journal - Abstract of article: Dominant and diet-responsive groups of bacteria within the human colonic microbiota

The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
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Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis

Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis | Bioinformatics and holobiota | Scoop.it
The human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status.
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Interconnected microbiomes and resistomes in low-income human habitats : Nature : Nature Research

Interconnected microbiomes and resistomes in low-income human habitats : Nature : Nature Research | Bioinformatics and holobiota | Scoop.it
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Gut microbiota in 2015: Prevotella in the gut: choose carefully : Nature Reviews Gastroenterology & Hepatology : Nature Research

Gut microbial communities often contain many Bacteroides or their close relatives, Prevotella, but not both. Prevotella strains are associated with plant-rich diets but are also linked with chronic inflammatory conditions. In 2015, papers probed the genomic diversity of Prevotella strains and interactions of Prevotella copri with its host and other bacteria.
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Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. - PubMed - NCBI

Gut. 2016 Jan;65(1):63-72. doi: 10.1136/gutjnl-2014-308209. Epub 2014 Nov 26. Comparative Study; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
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