Context and the human microbiome.

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

authors： Igartua C,Davenport ER,Gilad Y,Nicolae DL,Pinto J,Ober C

更新日期：2017-02-01 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

authors： Veach AM,Morris R,Yip DZ,Yang ZK,Engle NL,Cregger MA,Tschaplinski TJ,Schadt CW

更新日期：2019-05-18 00:00:00

abstract：BACKGROUND:Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processe...

journal_title：Microbiome

authors： Edlund A,Yang Y,Yooseph S,He X,Shi W,McLean JS

更新日期：2018-12-06 00:00:00

abstract：BACKGROUND:A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribo...

journal_title：Microbiome

authors： Gomez-Silvan C,Leung MHY,Grue KA,Kaur R,Tong X,Lee PKH,Andersen GL

更新日期：2018-04-16 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

authors： Walker AW,Martin JC,Scott P,Parkhill J,Flint HJ,Scott KP

更新日期：2015-06-22 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

authors： Nash AK,Auchtung TA,Wong MC,Smith DP,Gesell JR,Ross MC,Stewart CJ,Metcalf GA,Muzny DM,Gibbs RA,Ajami NJ,Petrosino JF

更新日期：2017-11-25 00:00:00

abstract：:Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this process to the microbial diversity and function in the receiving ecosystems. Currently used methods, i.e., counti...

journal_title：Microbiome

authors： Mei R,Liu WT

更新日期：2019-11-06 00:00:00

abstract：BACKGROUND:Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly c...

journal_title：Microbiome

authors： Gobet A,Mest L,Perennou M,Dittami SM,Caralp C,Coulombet C,Huchette S,Roussel S,Michel G,Leblanc C

更新日期：2018-03-27 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

authors： Yu K,Yi S,Li B,Guo F,Peng X,Wang Z,Wu Y,Alvarez-Cohen L,Zhang T

更新日期：2019-02-06 00:00:00

abstract：BACKGROUND:Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is availab...

journal_title：Microbiome

authors： Kim JY,Whon TW,Lim MY,Kim YB,Kim N,Kwon MS,Kim J,Lee SH,Choi HJ,Nam IH,Chung WH,Kim JH,Bae JW,Roh SW,Nam YD

更新日期：2020-08-04 00:00:00

abstract：BACKGROUND:High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The obje...

journal_title：Microbiome

authors： Liu J,Abdelfattah A,Norelli J,Burchard E,Schena L,Droby S,Wisniewski M

更新日期：2018-01-27 00:00:00

abstract：BACKGROUND:Clostridium difficile infection (CDI) is the leading infectious cause of nosocomial diarrhea. Hospitalized patients are at increased risk of developing CDI because they are exposed to C. difficile spores through contact with the hospital environment and often receive antibiotics and other medications that ca...

journal_title：Microbiome

authors： Vincent C,Miller MA,Edens TJ,Mehrotra S,Dewar K,Manges AR

更新日期：2016-03-14 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

authors： Liu YR,Delgado-Baquerizo M,Bi L,Zhu J,He JZ

更新日期：2018-10-18 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

authors： Kwak S,Choi J,Hink T,Reske KA,Blount K,Jones C,Bost MH,Sun X,Burnham CD,Dubberke ER,Dantas G,CDC Prevention Epicenter Program.

更新日期：2020-08-31 00:00:00

abstract：BACKGROUND:Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown. RESULTS:In this study,...

journal_title：Microbiome

authors： Che Y,Xia Y,Liu L,Li AD,Yang Y,Zhang T

更新日期：2019-03-21 00:00:00

abstract：BACKGROUND:Lower respiratory tract infection (LRTI) is a major contributor to respiratory failure requiring intubation and mechanical ventilation. LRTI also occurs during mechanical ventilation, increasing the morbidity and mortality of intubated patients. We sought to understand the dynamics of respiratory tract micro...

journal_title：Microbiome

authors： Kelly BJ,Imai I,Bittinger K,Laughlin A,Fuchs BD,Bushman FD,Collman RG

更新日期：2016-02-11 00:00:00

abstract：BACKGROUND:This proof-of-principle study examines whether postnatal, low-dose exposure to environmental chemicals modifies the composition of gut microbiome. Three chemicals that are widely used in personal care products-diethyl phthalate (DEP), methylparaben (MPB), triclosan (TCS)-and their mixture (MIX) were administ...

journal_title：Microbiome

authors： Hu J,Raikhel V,Gopalakrishnan K,Fernandez-Hernandez H,Lambertini L,Manservisi F,Falcioni L,Bua L,Belpoggi F,L Teitelbaum S,Chen J

更新日期：2016-06-14 00:00:00

abstract：BACKGROUND:Given their adaptation to nutrient-poor and drought environments, cycads are vital models for plant-microbiome interaction research because they are likely to host an important reservoir of beneficial microbes that may support cycad survival. However, a comprehensive understanding of the diversity and commun...

journal_title：Microbiome

authors： Zheng Y,Gong X

更新日期：2019-12-02 00:00:00

abstract：BACKGROUND:Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microb...

journal_title：Microbiome

authors： Liu YF,Galzerani DD,Mbadinga SM,Zaramela LS,Gu JD,Mu BZ,Zengler K

更新日期：2018-01-05 00:00:00

abstract：BACKGROUND:In microbiome studies, it is important to detect taxa which are associated with pathological outcomes at the lowest definable taxonomic rank, such as genus or species. Traditionally, taxa at the target rank are tested for individual association, followed by the Benjamini-Hochberg (BH) procedure to control fo...

journal_title：Microbiome

authors： Hu J,Koh H,He L,Liu M,Blaser MJ,Li H

更新日期：2018-07-25 00:00:00

abstract：BACKGROUND:Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method...

journal_title：Microbiome

authors： Gasc C,Peyret P

更新日期：2018-03-27 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

authors： Hong BY,Sobue T,Choquette L,Dupuy AK,Thompson A,Burleson JA,Salner AL,Schauer PK,Joshi P,Fox E,Shin DG,Weinstock GM,Strausbaugh LD,Dongari-Bagtzoglou A,Peterson DE,Diaz PI

更新日期：2019-04-25 00:00:00

abstract：BACKGROUND:pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to "spillover effects" on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarel...

journal_title：Microbiome

authors： Lammel DR,Barth G,Ovaskainen O,Cruz LM,Zanatta JA,Ryo M,de Souza EM,Pedrosa FO

更新日期：2018-06-11 00:00:00

abstract：BACKGROUND:The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, bu...

journal_title：Microbiome

authors： Pandit RJ,Hinsu AT,Patel NV,Koringa PG,Jakhesara SJ,Thakkar JR,Shah TM,Limon G,Psifidi A,Guitian J,Hume DA,Tomley FM,Rank DN,Raman M,Tirumurugaan KG,Blake DP,Joshi CG

更新日期：2018-06-23 00:00:00

abstract：:The human microbiome refers to the genetic composition of microorganisms in a particular location in the human body. Emerging evidence over the past many years suggests that the microbiome constitute drivers of human fate almost at par with our genome and epigenome. It is now well accepted after decades of disbelief t...

journal_title：Microbiome

authors： Silverstein RB,Mysorekar IU

更新日期：2021-01-12 00:00:00

abstract：BACKGROUND:Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the rec...

journal_title：Microbiome

authors： Lee STM,Kahn SA,Delmont TO,Shaiber A,Esen ÖC,Hubert NA,Morrison HG,Antonopoulos DA,Rubin DT,Eren AM

更新日期：2017-05-04 00:00:00

abstract：BACKGROUND:Bacterial vaginosis (BV), the most common vaginal condition of reproductive-aged women, is associated with a highly diverse and heterogeneous microbiota. Here we present a proof-of-principle analysis to uncover the function of the microbiota using meta-RNA-seq to uncover genes and pathways that potentially d...

journal_title：Microbiome

authors： Macklaim JM,Fernandes AD,Di Bella JM,Hammond JA,Reid G,Gloor GB

更新日期：2013-04-12 00:00:00

abstract：BACKGROUND:Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 t...

journal_title：Microbiome

authors： Minich JJ,Ali F,Marotz C,Belda-Ferre P,Chiang L,Shaffer JP,Carpenter CS,McDonald D,Gilbert J,Allard SM,Allen EE,Knight R,Sweeney DA,Swafford AD

更新日期：2021-01-22 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

authors： France MT,Ma B,Gajer P,Brown S,Humphrys MS,Holm JB,Waetjen LE,Brotman RM,Ravel J

更新日期：2020-11-23 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

authors： Zhang J,Gao Q,Zhang Q,Wang T,Yue H,Wu L,Shi J,Qin Z,Zhou J,Zuo J,Yang Y

更新日期：2017-05-31 00:00:00