Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility.

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:The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe inter...

journal_title：Microbiome

authors： Heinken A,Ravcheev DA,Baldini F,Heirendt L,Fleming RMT,Thiele I

更新日期：2019-05-15 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：:Human genome-wide association studies (GWASs) have recurrently estimated lower heritability estimates than familial studies. Many explanations have been suggested to explain these lower estimates, including that a substantial proportion of genetic variation and gene-by-environment interactions are unmeasured in typica...

journal_title：Microbiome

authors： Douglas GM,Bielawski JP,Langille MGI

更新日期：2020-06-08 00:00:00

abstract：BACKGROUND:In previous studies, the gram-positive firmicute genus Paenibacillus was found with significant abundances in nests of wild solitary bees. Paenibacillus larvae is well-known for beekeepers as a severe pathogen causing the fatal honey bee disease American foulbrood, and other members of the genus are either s...

journal_title：Microbiome

authors： Keller A,Brandel A,Becker MC,Balles R,Abdelmohsen UR,Ankenbrand MJ,Sickel W

更新日期：2018-12-22 00:00:00

abstract：BACKGROUND:Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Br...

journal_title：Microbiome

authors： Mu DS,Wang S,Liang QY,Du ZZ,Tian R,Ouyang Y,Wang XP,Zhou A,Gong Y,Chen GJ,Van Nostrand J,Yang Y,Zhou J,Du ZJ

更新日期：2020-08-31 00:00:00

abstract：BACKGROUND:The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of an...

journal_title：Microbiome

authors： Miller EA,Livermore JA,Alberts SC,Tung J,Archie EA

更新日期：2017-01-19 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: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: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: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

authors： Kazerouni A,Burgess J,Burns LJ,Wein LM

更新日期：2015-12-17 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: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

authors： Stanislawski MA,Dabelea D,Wagner BD,Sontag MK,Lozupone CA,Eggesbø M

更新日期：2017-09-04 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: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

authors： Farhan Ul Haque M,Crombie AT,Murrell JC

更新日期：2019-10-04 00:00:00

abstract：BACKGROUND:The interconnectivities of built and natural environments can serve as conduits for the proliferation and dissemination of antibiotic resistance genes (ARGs). Several studies have compared the broad spectrum of ARGs (i.e., "resistomes") in various environmental compartments, but there is a need to identify u...

journal_title：Microbiome

authors： Gupta S,Arango-Argoty G,Zhang L,Pruden A,Vikesland P

更新日期：2019-08-29 00:00:00

abstract：BACKGROUND:Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the...

journal_title：Microbiome

authors： Farhan Ul Haque M,Crombie AT,Ensminger SA,Baciu C,Murrell JC

更新日期：2018-06-28 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：:Following publication of the original article [1], the authors reported an error in Fig. 2. The original Fig. 2 has been incorrectly replaced with the Supplementary Fig. 2. The correct Fig. 2 is presented here. ...

journal_title：Microbiome

authors： Armstrong AJS,Shaffer M,Nusbacher NM,Griesmer C,Fiorillo S,Schneider JM,Neff CP,Li SX,Fontenot AP,Campbell T,Palmer BE,Lozupone CA

更新日期：2020-04-06 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

authors： Huang P,Zhang Y,Xiao K,Jiang F,Wang H,Tang D,Liu D,Liu B,Liu Y,He X,Liu H,Liu X,Qing Z,Liu C,Huang J,Ren Y,Yun L,Yin L,Lin Q,Zeng C,Su X,Yuan J,Lin L,Hu N,Cao H,Huang S,Guo Y,Fan W,Zeng J

更新日期：2018-11-27 00:00:00

abstract：BACKGROUND:The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk. RESULTS:The composition of bifidobacterial c...

journal_title：Microbiome

authors： Duranti S,Lugli GA,Mancabelli L,Armanini F,Turroni F,James K,Ferretti P,Gorfer V,Ferrario C,Milani C,Mangifesta M,Anzalone R,Zolfo M,Viappiani A,Pasolli E,Bariletti I,Canto R,Clementi R,Cologna M,Crifò T,Cusumano

更新日期：2017-06-26 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: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:Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the ge...

journal_title：Microbiome

authors： Hammond M,Homa F,Andersson-Svahn H,Ettema TJ,Joensson HN

更新日期：2016-10-06 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: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: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

authors： Minot SS,Willis AD

更新日期：2019-08-01 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

authors： Angly FE,Dennis PG,Skarshewski A,Vanwonterghem I,Hugenholtz P,Tyson GW

更新日期：2014-04-07 00:00:00

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

authors： LaPelusa M,Donoviel D,Branzini SE,Carlson PE Jr,Culler S,Cheema AK,Kaddurah-Daouk R,Kelly D,de Cremoux I,Knight R,Krajmalnik-Brown R,Mayo SL,Mazmanian SK,Mayer EA,Petrosino JF,Garrison K

更新日期：2021-01-04 00:00:00

abstract：BACKGROUND:Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in mo...

journal_title：Microbiome

authors： Levy Karin E,Mirdita M,Söding J

更新日期：2020-04-03 00:00:00