Abstract:
:Human microbiome reference datasets provide epidemiological context for researchers, enabling them to uncover new insights into their own data through meta-analyses. In addition, large and comprehensive reference sets offer a means to develop or test hypotheses and can pave the way for addressing practical study design considerations such as sample size decisions. We discuss the importance of reference sets in human microbiome research, limitations of existing resources, technical challenges to employing reference sets, examples of their usage, and contributions of the American Gut Project to the development of a comprehensive reference set. Through engaging the general public, the American Gut Project aims to address many of the issues present in existing reference resources, characterizing health and disease, lifestyle, and dietary choices of the participants while extending its efforts globally through international collaborations.
journal_name
Microbiomejournal_title
Microbiomeauthors
McDonald D,Birmingham A,Knight Rdoi
10.1186/s40168-015-0117-2subject
Has Abstractpub_date
2015-11-04 00:00:00pages
52issn
2049-2618pii
10.1186/s40168-015-0117-2journal_volume
3pub_type
杂志文章,评审相关文献
Microbiome文献大全abstract::The inaugural "Microbiome for Mars" virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duration human space travel. The conference focused on surveying current microbiome research, future endeavors, and h...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00951-5
更新日期:2021-01-04 00:00:00
abstract:BACKGROUND:The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known abou...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0170-5
更新日期:2016-06-16 00:00:00
abstract:BACKGROUND:Recent evidence supports that the maternal gut microbiota impacts the initial infant gut microbiota. Since the gut microbiota may play a causal role in the development of obesity, it is important to understand how pre-pregnancy weight and gestational weight gain (GWG) impact the gut microbiota of mothers at ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0332-0
更新日期:2017-09-04 00:00:00
abstract:BACKGROUND:Plants have developed defense strategies for phytopathogen and herbivore protection via coordinated metabolic mechanisms. Low-molecular weight metabolites produced within plant tissues, such as salicylic acid, represent one such mechanism which likely mediates plant - microbe interactions above and below gro...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0668-8
更新日期:2019-05-18 00:00:00
abstract:BACKGROUND:Bacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts....
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0272-8
更新日期:2017-05-31 00:00:00
abstract:BACKGROUND:The degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here, we performed a genetic mapping study of the microbiome in two accessible upper airway sites, the nasopharynx and the nasal vestibule, during two seasons in 144 adult members of a founder po...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0227-5
更新日期:2017-02-01 00:00:00
abstract:BACKGROUND:Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communiti...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0634-5
更新日期:2019-02-06 00:00:00
abstract:BACKGROUND:Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata extract (MCE), with effective ingredients of benzylisoquinoline alkaloids, is a potential alternativ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0590-5
更新日期:2018-11-27 00:00:00
abstract:BACKGROUND:Fecal microbiota transplantation is an effective treatment for recurrent Clostridium difficile infection and is being investigated as a treatment for other microbiota-associated diseases. To facilitate these activities, an international public stool bank has been created, which screens donors and processes s...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-015-0140-3
更新日期:2015-12-17 00:00:00
abstract:BACKGROUND:Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, pla...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0741-3
更新日期:2019-10-04 00:00:00
abstract:BACKGROUND:Parkinson's disease (PD) is a neurodegenerative disorder with no absolute cure. The evidence of the involvement of gut microbiota in PD pathogenesis suggests the need to identify certain molecule(s) derived from the gut microbiota, which has the potential to manage PD. Osteocalcin (OCN), an osteoblast-secret...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00988-6
更新日期:2021-01-31 00:00:00
abstract:BACKGROUND:The use of culture-independent nucleic acid techniques, such as ribosomal RNA gene cloning library analysis, has unveiled the tremendous microbial diversity that exists in natural environments. In sharp contrast to this great achievement is the current difficulty in cultivating the majority of bacterial spec...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/2049-2618-1-4
更新日期:2013-01-09 00:00:00
abstract:BACKGROUND:The microbial populations of the human intestinal tract and their relationship to specific diseases have been extensively studied during the last decade. However, the characterization of the human bile microbiota as a whole has been hampered by difficulties in accessing biological samples and the lack of ade...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0712-8
更新日期:2019-07-04 00:00:00
abstract:BACKGROUND:Post-infarction cardiovascular remodeling and heart failure are the leading cause of myocardial infarction (MI)-driven death during the past decades. Experimental observations have involved intestinal microbiota in the susceptibility to MI in mice; however, in humans, identifying whether translocation of gut...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0441-4
更新日期:2018-04-03 00:00:00
abstract:BACKGROUND:Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulo...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0629-2
更新日期:2019-02-01 00:00:00
abstract:BACKGROUND:Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0451-2
更新日期:2018-04-11 00:00:00
abstract:BACKGROUND:Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epide...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00934-6
更新日期:2020-11-23 00:00:00
abstract:BACKGROUND:Whole-genome "shotgun" (WGS) metagenomic sequencing is an increasingly widely used tool for analyzing the metagenomic content of microbiome samples. While WGS data contains gene-level information, it can be challenging to analyze the millions of microbial genes which are typically found in microbiome experim...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0722-6
更新日期:2019-08-01 00:00:00
abstract:BACKGROUND:Aphids are known to live in symbiosis with specific bacteria, called endosymbionts which can be classified as obligate or accessory. Buchnera aphidicola is generally the only obligatory symbiont present in aphids, supplying essential nutrients that are missing in the plants phloem to its host. Pentalonia nig...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-015-0130-5
更新日期:2015-12-15 00:00:00
abstract:BACKGROUND:Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease c...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0373-4
更新日期:2017-11-25 00:00:00
abstract:BACKGROUND:Intestinal microbiota restoration can be achieved by complementing a subject's perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic-resistant genes (ARGs...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00907-9
更新日期:2020-08-31 00:00:00
abstract:BACKGROUND:The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulatin...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0572-7
更新日期:2018-10-18 00:00:00
abstract:BACKGROUND:Culture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between species. RESULTS:Based on 2,900 sequenced reference genomes, we show that 16S rRNA gene copy number (GC...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/2049-2618-2-11
更新日期:2014-04-07 00:00:00
abstract:BACKGROUND:Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associated Gammaproteobacteria in very low birth weight (VLBW) infants. Fecal microbiome was characterized ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0547-8
更新日期:2018-09-12 00:00:00
abstract:BACKGROUND:Characterisation of the bacterial composition of the gut microbiota is increasingly carried out with a view to establish the role of different bacterial species in causation or prevention of disease. It is thus essential that the methods used to determine the microbial composition are robust. Here, several w...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-015-0087-4
更新日期:2015-06-22 00:00:00
abstract:BACKGROUND:A westernized diet comprising a high caloric intake from animal fats is known to influence the development of pathological inflammatory conditions. However, there has been relatively little focus upon the implications of such diets for the progression of infectious disease. Here, we investigated the influenc...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0621-x
更新日期:2019-01-18 00:00:00
abstract:BACKGROUND:The newborn mammal is rapidly colonized by a complex microbial community, whose importance for host health is becoming increasingly clear. Understanding the forces that shape the early community, especially during the nursing period, is critical to gain insight into how this consortium of microbes is assembl...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-015-0091-8
更新日期:2015-07-01 00:00:00
abstract:BACKGROUND:Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeot...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0181-2
更新日期:2016-07-07 00:00:00
abstract:BACKGROUND:Current knowledge of the urinary tract microbiome is limited to urine analysis and analysis of biofilms formed on Foley catheters. Bacterial biofilms on ureteral stents have rarely been investigated, and no cultivation-independent data are available on the microbiome of the encrustations on the stents. RESU...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0674-x
更新日期:2019-04-13 00:00:00
abstract:BACKGROUND:Gastrointestinal mucosal injury (mucositis), commonly affecting the oral cavity, is a clinically significant yet incompletely understood complication of cancer chemotherapy. Although antineoplastic cytotoxicity constitutes the primary injury trigger, the interaction of oral microbial commensals with mucosal ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0679-5
更新日期:2019-04-25 00:00:00