The human microbiome: at the interface of health and disease

Nature Reviews Genetics, Год журнала: 2012, Номер 13(4), С. 260 - 270

Опубликована: Март 13, 2012

Язык: Английский

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Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy

Cell, Год журнала: 2012, Номер 150(3), С. 470 - 480

Опубликована: Авг. 1, 2012

Язык: Английский

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Defining the human microbiome

Nutrition Reviews, Год журнала: 2012, Номер 70, С. S38 - S44

Опубликована: Авг. 1, 2012

Rapidly developing sequencing methods and analytical techniques are enhancing our ability to understand the human microbiome, and, indeed, how microbiome its constituents defined. This review highlights recent research that expands on different spatial temporal scales, including daily time series datasets spanning months. Furthermore, emerging concepts related defining operational taxonomic units, diversity indices, core versus transient microbiomes, possibility of enterotypes discussed. Additional advances in technology understanding will provide exciting prospects for exploiting microbiota personalized medicine.

Язык: Английский

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Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

Microbiome, Год журнала: 2014, Номер 2(1)

Опубликована: Май 5, 2014

Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA (RNA-seq), chromatin immunoprecipitation (ChIP-seq), 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. In each case the underlying data are similar composed counts reads mapped a large number features in sample. Despite this similarity, methods used for these experimental all different, do not translate across Alternative have been developed physical geological sciences treat as compositions. Compositional transform relative abundances with result analyses more robust reproducible.Data from an vitro experiment, RNA-seq experiment Human Microbiome Project abundance dataset were examined by ALDEx2, compositional tool uses Bayesian infer technical statistical error. The ALDEx2 approach is shown be suitable three types data: it correctly identifies both direction differential substantially set differentially expressed genes leading tools taxa distinguish tongue dorsum buccal mucosa dataset. design reduces false positive identifications many few samples.Statistical per feature showed R package simple tool, which can applied RNA-seq, datasets, extension other techniques use approach.

Язык: Английский

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Gut Microbes and the Brain: Paradigm Shift in Neuroscience

Journal of Neuroscience, Год журнала: 2014, Номер 34(46), С. 15490 - 15496

Опубликована: Ноя. 12, 2014

The discovery of the size and complexity human microbiome has resulted in an ongoing reevaluation many concepts health disease, including diseases affecting CNS. A growing body preclinical literature demonstrated bidirectional signaling between brain gut microbiome, involving multiple neurocrine endocrine mechanisms. While psychological physical stressors can affect composition metabolic activity microbiota, experimental changes to emotional behavior related systems. These findings have speculation that alterations may play a pathophysiological role diseases, autism spectrum disorder, anxiety, depression, chronic pain. Ongoing large-scale population-based studies imaging looking at effect modulation on responses emotion-related stimuli are seeking validate these speculations. This article is summary emerging topics covered symposium not meant be comprehensive review subject.

Язык: Английский

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The infant microbiome development: mom matters

Trends in Molecular Medicine, Год журнала: 2014, Номер 21(2), С. 109 - 117

Опубликована: Дек. 11, 2014

Язык: Английский

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The Intestinal Microbiome in Early Life: Health and Disease

Frontiers in Immunology, Год журнала: 2014, Номер 5

Опубликована: Сен. 5, 2014

Human microbial colonization begins at birth and continues to develop modulate in species abundance for about three years, until the microbiota becomes adult-like. During same time period, children experience significant developmental changes that influence their current health status as well immune system. An ever-expanding number of articles associate several diseases with early life imbalances gut microbiota, also referred dysbiosis. Whether dysbiosis precedes plays a role disease pathogenesis, or simply originates from process itself is question beginning be answered few diseases, including IBD, obesity asthma. This review describes microbiome structure function during formative first years life, environmental factors determine its composition. It aims discuss recent advances understanding development immune-mediated, metabolic, neurological diseases. A greater how impacts our could potentially lead novel microbial-derived therapies target prevention an age.

Язык: Английский

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Fecal Microbiota and Metabolome of Children with Autism and Pervasive Developmental Disorder Not Otherwise Specified

PLoS ONE, Год журнала: 2013, Номер 8(10), С. e76993 - e76993

Опубликована: Окт. 9, 2013

This study aimed at investigating the fecal microbiota and metabolome of children with Pervasive Developmental Disorder Not Otherwise Specified (PDD-NOS) autism (AD) in comparison to healthy (HC). Bacterial tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) 16S rDNA rRNA analyses were carried out determine total bacteria (16S rDNA) metabolically active rRNA), respectively. The main bacterial phyla (Firmicutes, Bacteroidetes, Fusobacteria Verrucomicrobia) significantly (P<0.05) changed among three groups children. As estimated by rarefaction, Chao Shannon diversity index, highest microbial was found AD Based on 16S-rRNA culture-dependent data, Faecalibacterium Ruminococcus present level samples PDD-NOS HC Caloramator, Sarcina Clostridium genera Compared HC, composition Lachnospiraceae family also differed and, especially, Except for Eubacterium siraeum, lowest Eubacteriaceae Bacteroidetes some Alistipes Akkermansia species almost or as well all identified Sutterellaceae Enterobacteriaceae AD. children, Bifidobacterium decreased shown Canonical Discriminant Analysis Principal Coordinates, levels free amino acids volatile organic compounds markedly affected If gut differences are one concomitant causes consequence autism, they may have implications regarding specific diagnostic test, and/or treatment prevention.

Язык: Английский

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Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

Biochemical and Biophysical Research Communications, Год журнала: 2015, Номер 469(4), С. 967 - 977

Опубликована: Дек. 22, 2015

Язык: Английский

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Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ

Therapeutic Advances in Gastroenterology, Год журнала: 2013, Номер 6(4), С. 295 - 308

Опубликована: Март 26, 2013

The human gut microbiota has become the subject of extensive research in recent years and our knowledge resident species their potential functional capacity is rapidly growing. Our harbours a complex community over 100 trillion microbial cells which influence physiology, metabolism, nutrition immune function while disruption to been linked with gastrointestinal conditions such as inflammatory bowel disease obesity. Here, we review many significant studies that have centred on further enhancing understanding complexity intestinal communities well genetic metabolic potential. These provided important information respect what constitutes ‘healthy microbiota’ furthering role microbes diseases. We also highlight recently developed genomic other tools are used study microbiome and, finally, consider manipulation therapeutic option treat chronic disease.

Язык: Английский

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