Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.

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: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

authors： Gao W,Navarroli D,Naimark J,Zhang W,Chao SH,Meldrum DR

更新日期：2013-01-09 00:00:00

abstract：:The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relationship, a holistic view of the gut microbiota-host association imposes itself. Ideally, a stable state of equ...

journal_title：Microbiome

authors： van de Guchte M,Blottière HM,Doré J

更新日期：2018-05-01 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

authors： Shi W,Li M,Wei G,Tian R,Li C,Wang B,Lin R,Shi C,Chi X,Zhou B,Gao Z

更新日期：2019-02-01 00:00:00

abstract：:Recent studies have conflicting data regarding the presence of intra-amniotic microbiota. Viral communities are increasingly recognized as important although overlooked components of the human microbiota. It is unknown if the developing fetus is exposed to a community of viruses (virome). Given the debate over the exi...

journal_title：Microbiome

authors： Lim ES,Rodriguez C,Holtz LR

更新日期：2018-05-11 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:Increasing evidence reveals the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT), i.e., a replacement of the cellular components of the ...

journal_title：Microbiome

authors： Ingham AC,Kielsen K,Cilieborg MS,Lund O,Holmes S,Aarestrup FM,Müller KG,Pamp SJ

更新日期：2019-09-13 00:00:00

abstract：BACKGROUND:Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on ...

journal_title：Microbiome

authors： Velsko IM,Fellows Yates JA,Aron F,Hagan RW,Frantz LAF,Loe L,Martinez JBR,Chaves E,Gosden C,Larson G,Warinner C

更新日期：2019-07-06 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:Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of Califo...

journal_title：Microbiome

authors： Dombrowski N,Seitz KW,Teske AP,Baker BJ

更新日期：2017-08-23 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: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: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:Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducted a comprehensive study of gut microbiota of a well-studied North American red squirrel (Tamiasciuru...

journal_title：Microbiome

authors： Ren T,Boutin S,Humphries MM,Dantzer B,Gorrell JC,Coltman DW,McAdam AG,Wu M

更新日期：2017-12-21 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: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

authors： Ho TTB,Groer MW,Kane B,Yee AL,Torres BA,Gilbert JA,Maheshwari A

更新日期：2018-09-12 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: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: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

authors： Buhmann MT,Abt D,Nolte O,Neu TR,Strempel S,Albrich WC,Betschart P,Zumstein V,Neels A,Maniura-Weber K,Ren Q

更新日期：2019-04-13 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: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:Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indigenous populations is required to advance treatment and reduce prevalence. We conducted a systematic ...

journal_title：Microbiome

authors： Coleman A,Wood A,Bialasiewicz S,Ware RS,Marsh RL,Cervin A

更新日期：2018-11-05 00:00:00

abstract：BACKGROUND:Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into nat...

journal_title：Microbiome

authors： Wicaksono WA,Kusstatscher P,Erschen S,Reisenhofer-Graber T,Grube M,Cernava T,Berg G

更新日期：2021-01-27 00:00:00

abstract：BACKGROUND:The role of the gut microbiome in arresting pathogen colonization and growth is important for protection against Clostridium difficile infection (CDI). Observational studies associate proton pump inhibitor (PPI) use and CDI incidence. We hypothesized that PPI use affected the distal gut microbiome over time,...

journal_title：Microbiome

authors： Seto CT,Jeraldo P,Orenstein R,Chia N,DiBaise JK

更新日期：2014-11-25 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

authors： De Clerck C,Fujiwara A,Joncour P,Léonard S,Félix ML,Francis F,Jijakli MH,Tsuchida T,Massart S

更新日期：2015-12-15 00:00:00

abstract：BACKGROUND:High-throughput bacterial 16S rRNA gene sequencing followed by clustering of short sequences into operational taxonomic units (OTUs) is widely used for microbiome profiling. However, clustering of short 16S rRNA gene reads into biologically meaningful OTUs is challenging, in part because nucleotide variation...

journal_title：Microbiome

authors： Franzén O,Hu J,Bao X,Itzkowitz SH,Peter I,Bashir A

更新日期：2015-10-05 00:00:00

abstract：BACKGROUND:Periodontitis is an infectious and inflammatory disease of polymicrobial etiology that can lead to the destruction of bones and tissues that support the teeth. The management of chronic periodontitis (CP) relies heavily on elimination or at least control of known pathogenic consortia associated with the dise...

journal_title：Microbiome

authors： Galimanas V,Hall MW,Singh N,Lynch MD,Goldberg M,Tenenbaum H,Cvitkovitch DG,Neufeld JD,Senadheera DB

更新日期：2014-08-26 00:00:00

abstract：BACKGROUND:The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and...

journal_title：Microbiome

authors： Rausch P,Rühlemann M,Hermes BM,Doms S,Dagan T,Dierking K,Domin H,Fraune S,von Frieling J,Hentschel U,Heinsen FA,Höppner M,Jahn MT,Jaspers C,Kissoyan KAB,Langfeldt D,Rehman A,Reusch TBH,Roeder T,Schmitz RA,Schulenb

更新日期：2019-09-14 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:Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and i...

journal_title：Microbiome

authors： Kamke J,Kittelmann S,Soni P,Li Y,Tavendale M,Ganesh S,Janssen PH,Shi W,Froula J,Rubin EM,Attwood GT

更新日期：2016-10-19 00:00:00