CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

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: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: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: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

authors： Molinero N,Ruiz L,Milani C,Gutiérrez-Díaz I,Sánchez B,Mangifesta M,Segura J,Cambero I,Campelo AB,García-Bernardo CM,Cabrera A,Rodríguez JI,González S,Rodríguez JM,Ventura M,Delgado S,Margolles A

更新日期：2019-07-04 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

authors： Hou YF,Shan C,Zhuang SY,Zhuang QQ,Ghosh A,Zhu KC,Kong XK,Wang SM,Gong YL,Yang YY,Tao B,Sun LH,Zhao HY,Guo XZ,Wang WQ,Ning G,Gu YY,Li ST,Liu JM

更新日期：2021-01-31 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: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: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:Metallo-β-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly proble...

journal_title：Microbiome

authors： Berglund F,Marathe NP,Österlund T,Bengtsson-Palme J,Kotsakis S,Flach CF,Larsson DGJ,Kristiansson E

更新日期：2017-10-12 00:00:00

abstract：BACKGROUND:The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two...

journal_title：Microbiome

authors： Haro-Moreno JM,López-Pérez M,de la Torre JR,Picazo A,Camacho A,Rodriguez-Valera F

更新日期：2018-07-10 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: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: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

authors： Ormerod KL,Wood DL,Lachner N,Gellatly SL,Daly JN,Parsons JD,Dal'Molin CG,Palfreyman RW,Nielsen LK,Cooper MA,Morrison M,Hansbro PM,Hugenholtz P

更新日期：2016-07-07 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

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：:Chronic inflammation represents one of the most consistent biologic features of aging. However, the precise etiology of persistent low-grade increases in inflammation remains unclear. Recent evidence suggests that the gut microbiome may play a key role in age-related inflammation. Indeed, several studies have indicate...

journal_title：Microbiome

authors： Buford TW

更新日期：2017-07-14 00:00:00

abstract：BACKGROUND:The study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that dete...

journal_title：Microbiome

authors： Miletto M,Lindow SE

更新日期：2015-12-10 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: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:Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms. RESULTS:Here we introduce CloVR-ITS, an automated pipeline ...

journal_title：Microbiome

authors： White JR,Maddox C,White O,Angiuoli SV,Fricke WF

更新日期：2013-02-04 00:00:00

abstract：BACKGROUND:The development of the rumen is an important physiological challenge for young ruminants. Previous studies have shown that starter feeding can effectively facilitate the growth and development of the rumen in ruminants. However, the mechanism through which starter feeding stimulates the development of the ru...

journal_title：Microbiome

authors： Lin L,Xie F,Sun D,Liu J,Zhu W,Mao S

更新日期：2019-06-03 00:00:00

abstract：BACKGROUND:There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacture...

journal_title：Microbiome

authors： Chopyk J,Chattopadhyay S,Kulkarni P,Claye E,Babik KR,Reid MC,Smyth EM,Hittle LE,Paulson JN,Cruz-Cano R,Pop M,Buehler SS,Clark PI,Sapkota AR,Mongodin EF

更新日期：2017-02-15 00:00:00

abstract：BACKGROUND:Campylobacter jejuni is the leading antecedent infection to the autoimmune neuropathy Guillain-Barré syndrome (GBS), which is accompanied by an autoimmune anti-ganglioside antibody attack on peripheral nerves. Previously, we showed that contrasting immune responses mediate C. jejuni induced colitis and autoi...

journal_title：Microbiome

authors： Brooks PT,Brakel KA,Bell JA,Bejcek CE,Gilpin T,Brudvig JM,Mansfield LS

更新日期：2017-08-08 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: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: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

authors： Pérez-Losada M,Crandall KA,Freishtat RJ

更新日期：2016-06-16 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:Disruption of the gut microbiota homeostasis may induce low-grade inflammation leading to obesity-associated diseases. A major protective mechanism is to use the multi-layered mucus structures to keep a safe distance between gut epithelial cells and microbiota. To investigate whether pesticides would induce ...

journal_title：Microbiome

authors： Liang Y,Zhan J,Liu D,Luo M,Han J,Liu X,Liu C,Cheng Z,Zhou Z,Wang P

更新日期：2019-02-11 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: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

authors： Frese SA,Parker K,Calvert CC,Mills DA

更新日期：2015-07-01 00:00:00

abstract：:An amendment to this paper has been published and can be accessed via the original article. ...

journal_title：Microbiome

authors： Berg G,Rybakova D,Fischer D,Cernava T,Vergès MC,Charles T,Chen X,Cocolin L,Eversole K,Corral GH,Kazou M,Kinkel L,Lange L,Lima N,Loy A,Macklin JA,Maguin E,Mauchline T,McClure R,Mitter B,Ryan M,Sarand I,Smidt H

更新日期：2020-08-20 00:00:00