Abstract:
BACKGROUND:Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors. RESULTS:Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate. CONCLUSIONS:Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Woodhams DC,Bletz MC,Becker CG,Bender HA,Buitrago-Rosas D,Diebboll H,Huynh R,Kearns PJ,Kueneman J,Kurosawa E,LaBumbard BC,Lyons C,McNally K,Schliep K,Shankar N,Tokash-Peters AG,Vences M,Whetstone Rdoi
10.1186/s13059-019-1908-8subject
Has Abstractpub_date
2020-02-03 00:00:00pages
23issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-019-1908-8journal_volume
21pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-s2-s12
更新日期:2008-01-01 00:00:00
abstract::Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1238-7
更新日期:2017-05-22 00:00:00
abstract:BACKGROUND:Gene duplication followed by divergence is one of the main sources of metabolic versatility. The patchwork and stepwise models of metabolic evolution help us to understand these processes, but their assumptions are relatively simplistic. We used a network-based approach to determine the influence of metaboli...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-2-r26
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:The cellular mechanisms that underlie metal toxicity and detoxification are rather variegated and incompletely understood. Genomic phenotyping was used to assess the roles played by all nonessential Saccharomyces cerevisiae proteins in modulating cell viability after exposure to cadmium, nickel, and other me...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-4-r67
更新日期:2008-04-07 00:00:00
abstract::Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/s13059-014-0516-x
更新日期:2014-11-08 00:00:00
abstract::A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs). ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1502-5
更新日期:2018-08-14 00:00:00
abstract::Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish bo...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-017-1236-9
更新日期:2017-05-23 00:00:00
abstract:BACKGROUND:DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1509-y
更新日期:2018-09-10 00:00:00
abstract::Extracting biological information from microarray data requires appropriate statistical methods. The simplest statistical method for detecting differential expression is the t test, which can be used to compare two conditions when there is replication of samples. With more than two conditions, analysis of variance (AN...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2003-4-4-210
更新日期:2003-01-01 00:00:00
abstract:BACKGROUND:During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-2-r11
更新日期:2012-02-20 00:00:00
abstract:BACKGROUND:The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functio...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0780-4
更新日期:2015-10-21 00:00:00
abstract:BACKGROUND:Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1701-8
更新日期:2019-05-20 00:00:00
abstract:BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-6-r69
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:The human genome contains "dark" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease. Here, we identify regions with few mappable reads ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1707-2
更新日期:2019-05-20 00:00:00
abstract::Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for e...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1758-4
更新日期:2019-09-02 00:00:00
abstract::Through understanding the intricacies of host-pathogen interactions, it is now possible to inhibit the growth of microbes, especially viruses, by targeting host-cell proteins and functions. This new antimicrobial strategy has proved effective in the laboratory and in the clinic, and it has great potential for the futu...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2006-7-1-201
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications mus...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02190-1
更新日期:2020-11-25 00:00:00
abstract:BACKGROUND:Structural variations (SVs) or copy number variations (CNVs) greatly impact the functions of the genes encoded in the genome and are responsible for diverse human diseases. Although a number of existing SV detection algorithms can detect many types of SVs using whole genome sequencing (WGS) data, no single a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1720-5
更新日期:2019-06-03 00:00:00
abstract::We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1880-3
更新日期:2019-12-20 00:00:00
abstract::Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1642-2
更新日期:2019-02-26 00:00:00
abstract::The honey bee Apis mellifera displays the most complex behavior of any insect. This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further enabled by the release of the honey-bee genome sequence. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-10-239
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1226-y
更新日期:2017-05-31 00:00:00
abstract:BACKGROUND:Alcoholism presents widespread social and human health problems. Alcohol sensitivity, the development of tolerance to alcohol and susceptibility to addiction vary in the population. Genetic factors that predispose to alcoholism remain largely unknown due to extensive genetic and environmental variation in hu...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-10-r95
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CREB (cAMP response element-binding protein), and microRNAs (miRNAs). How these two classes of regul...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-9-r85
更新日期:2006-01-01 00:00:00
abstract::Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. ...
journal_title:Genome biology
pub_type: 历史文章,杂志文章,评审
doi:10.1186/s13059-015-0866-z
更新日期:2016-01-11 00:00:00
abstract::Genome editing holds remarkable promise to transform human medicine as new therapies that can directly address the genetic causes of disease. However, concerns remain about possible undesired biological consequences of genome editors, particularly the introduction of unintended 'off-target' mutations. Here, we discuss...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1610-2
更新日期:2018-12-22 00:00:00
abstract:BACKGROUND:Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to s...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02192-z
更新日期:2020-11-23 00:00:00
abstract::The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter an...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1488-z
更新日期:2018-09-03 00:00:00
abstract:BACKGROUND:Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alp...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02080-6
更新日期:2020-07-02 00:00:00
abstract::Circular RNAs (circRNAs) are a new class of non-polyadenylated non-coding RNAs that may play important roles in many biological processes. Here we develop a single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) method to sequence both polyadenylated and non-polyadenylated RNAs from individual cells. Thi...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0706-1
更新日期:2015-07-23 00:00:00