Exploring Linkages between Taxonomic and Functional Profiles of the Human Microbiome.

abstract：:Bacterial motility is thought to play an important role in virulence. We have previously shown that proficient bacterial swimming and swarming in vitro is correlated with the persistent intramammary infection phenotype observed in cattle. However, little is known about the gene regulation differences important for dif...

journal_title：mSystems

authors： Lippolis JD,Brunelle BW,Reinhardt TA,Sacco RE,Thacker TC,Looft TP,Casey TA

更新日期：2016-08-09 00:00:00

abstract：:Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization-what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spe...

journal_title：mSystems

authors： Theis KR,Dheilly NM,Klassen JL,Brucker RM,Baines JF,Bosch TC,Cryan JF,Gilbert SF,Goodnight CJ,Lloyd EA,Sapp J,Vandenkoornhuyse P,Zilber-Rosenberg I,Rosenberg E,Bordenstein SR

更新日期：2016-03-29 00:00:00

abstract：:Recent studies of mammalian microbiomes have identified strong phylogenetic effects on bacterial community composition. Bats (Mammalia: Chiroptera) are among the most speciose mammals on the planet and the only mammal capable of true flight. We examined 1,236 16S rRNA amplicon libraries of the gut, oral, and skin micr...

journal_title：mSystems

authors： Lutz HL,Jackson EW,Webala PW,Babyesiza WS,Kerbis Peterhans JC,Demos TC,Patterson BD,Gilbert JA

更新日期：2019-11-12 00:00:00

abstract：:Trauma patients (TPs) are highly susceptible to infections, which often lead to sepsis. Among the numerous causative agents, Pseudomonas aeruginosa is especially important, as P. aeruginosa sepsis is often fatal. Understanding the mechanism of its pathogenesis in bloodstream infections is imperative; however, this mec...

journal_title：mSystems

authors： Elmassry MM,Mudaliar NS,Kottapalli KR,Dissanaike S,Griswold JA,San Francisco MJ,Colmer-Hamood JA,Hamood AN

更新日期：2019-05-07 00:00:00

abstract：:Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depe...

journal_title：mSystems

authors： Rodriguez-R LM,Gunturu S,Tiedje JM,Cole JR,Konstantinidis KT

更新日期：2018-04-10 00:00:00

abstract：:A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analy...

journal_title：mSystems

authors： Mageeney CM,Mohammed HT,Dies M,Anbari S,Cudkevich N,Chen Y,Buceta J,Ware VC

更新日期：2020-10-06 00:00:00

abstract：:Methylobacter species, members of the Methylococcales, have recently emerged as some of the globally widespread, cosmopolitan species that play a key role in the environmental consumption of methane across gradients of dioxygen tensions. In this work, we approached the question of how Methylobacter copes with hypoxia,...

journal_title：mSystems

authors： Yu Z,Pesesky M,Zhang L,Huang J,Winkler M,Chistoserdova L

更新日期：2020-01-21 00:00:00

abstract：:Intestinal bacterial dysbiosis has been increasingly linked to ankylosing spondylitis (AS), which is a prototypic and best studied subtype of spondyloarthritis (SpA). Fungi and bacteria coexist in the human gut and interact with each other. Although they have been shown to contribute actively to health or disease, no ...

journal_title：mSystems

authors： Li M,Dai B,Tang Y,Lei L,Li N,Liu C,Ge T,Zhang L,Xu Y,Hu Y,Li P,Zhang Y,Yuan J,Li X

更新日期：2019-03-26 00:00:00

abstract：:Many pathogenic bacteria of the family Enterobacteriaceae use type III secretion systems to inject virulence proteins, termed "effectors," into the host cell cytosol. Although host-cellular activities of several effectors have been demonstrated, the function and host-targeted pathways of most of the effectors identifi...

journal_title：mSystems

authors： Sontag RL,Nakayasu ES,Brown RN,Niemann GS,Sydor MA,Sanchez O,Ansong C,Lu SY,Choi H,Valleau D,Weitz KK,Savchenko A,Cambronne ED,Adkins JN

更新日期：2016-07-12 00:00:00

abstract：:Bisphenol A (BPA) accumulates in the maturing gut and liver in utero and is known to alter gut bacterial profiles in offspring. Gut bacterial dysbiosis may contribute to chronic colonic and systemic inflammation. We hypothesized that perinatal BPA exposure-induced intestinal (and liver) inflammation in offspring is du...

journal_title：mSystems

authors： Reddivari L,Veeramachaneni DNR,Walters WA,Lozupone C,Palmer J,Hewage MKK,Bhatnagar R,Amir A,Kennett MJ,Knight R,Vanamala JKP

更新日期：2017-10-10 00:00:00

abstract：:Apoptosis is generally considered the first line of defense against viral infection. However, the role of apoptosis in the interactions between plant viruses and their insect vectors has rarely been investigated. By studying plant DNA viruses of the genus Begomovirus within the family Geminiviridae, which are transmit...

journal_title：mSystems

authors： Wang XR,Wang C,Ban FX,Ghanim M,Pan LL,Qian LX,Liu YQ,Wang XW,Liu SS

更新日期：2020-09-22 00:00:00

abstract：:The identification of ancestral traits is essential to understanding the evolution of any group. In the case of parasitic groups, this helps us understand the adaptation to this lifestyle and a particular host. Most diplomonads are parasites, but there are free-living members of the group nested among the host-associa...

journal_title：mSystems

authors： Jiménez-González A,Andersson JO

更新日期：2020-12-22 00:00:00

abstract：:In bacterial cells, inhibition of ribosomes by sublethal concentrations of antibiotics leads to a decrease in the growth rate despite an increase in ribosome content. The limitation of ribosomal activity results in an increase in the level of expression from ribosomal promoters; this can deplete the pool of RNA polyme...

journal_title：mSystems

authors： Zhang Q,Brambilla E,Li R,Shi H,Cosentino Lagomarsino M,Sclavi B

更新日期：2020-09-08 00:00:00

abstract：:Health-associated oral Streptococcus species are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral pr...

journal_title：mSystems

authors： Velsko IM,Chakraborty B,Nascimento MM,Burne RA,Richards VP

更新日期：2018-12-18 00:00:00

abstract：:Vitamin B12 is synthesized by prokaryotes in the rumens of dairy cows-and this has implications in human nutrition since humans rely on consumption of dairy products for vitamin B12 acquisition. However, the concentration of vitamin B12 in milk is highly variable, and there is interest in determining what causes vitam...

journal_title：mSystems

authors： Franco-Lopez J,Duplessis M,Bui A,Reymond C,Poisson W,Blais L,Chong J,Gervais R,Rico DE,Cue RI,Girard CL,Ronholm J

更新日期：2020-03-03 00:00:00

abstract：:High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically ass...

journal_title：mSystems

authors： Rubbens P,Schmidt ML,Props R,Biddanda BA,Boon N,Waegeman W,Denef VJ

更新日期：2019-09-10 00:00:00

abstract：:Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and ge...

journal_title：mSystems

authors： Hynson NA,Frank KL,Alegado RA,Amend AS,Arif M,Bennett GM,Jani AJ,Medeiros MCI,Mileyko Y,Nelson CE,Nguyen NH,Nigro OD,Prisic S,Shin S,Takagi D,Wilson ST,Yew JY

更新日期：2018-03-13 00:00:00

abstract：:Dietary intake is difficult to measure reliably in humans because approaches typically rely on self-reporting, which can be incomplete and biased. In field studies of animals, DNA sequencing-based approaches such as metabarcoding have been developed to characterize diets, but such approaches have not previously been w...

journal_title：mSystems

authors： Reese AT,Kartzinel TR,Petrone BL,Turnbaugh PJ,Pringle RM,David LA

更新日期：2019-10-08 00:00:00

abstract：:Streptococcus mutans is a Gram-positive bacterium that thrives under acidic conditions and is a primary cause of tooth decay (dental caries). To better understand the metabolism of S. mutans on a systematic level, we manually constructed a genome-scale metabolic model of the S. mutans type strain UA159. The model, cal...

journal_title：mSystems

authors： Jijakli K,Jensen PA

更新日期：2019-10-29 00:00:00

abstract：:As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored "differential coverage binning" method on 22-Gb metagenomic sequences, we re...

journal_title：mSystems

authors： Tian RM,Zhang W,Cai L,Wong YH,Ding W,Qian PY

更新日期：2017-03-21 00:00:00

abstract：:Quantitative understanding and prediction of microbial community dynamics are an outstanding challenge. We test the hypothesis that metabolic mechanisms provide a foundation for accurate prediction of dynamics in microbial systems. In our research, metabolic models have been able to accurately predict species interact...

journal_title：mSystems

authors： Chacón JM,Harcombe WR

更新日期：2019-06-11 00:00:00

abstract：:Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical focus on the dominant...

journal_title：mSystems

authors： Khanolkar RA,Clark ST,Wang PW,Hwang DM,Yau YCW,Waters VJ,Guttman DS

更新日期：2020-12-01 00:00:00

abstract：:Globally, dental caries is the most prevalent chronic oral disease and affects roughly half of all children. The aim of this report was to use metagenomic analyses to investigate the relationship between the oral microbiome and caries in preschool children. A total of 25 preschoolers, aged 3 to 5 years old with severe...

journal_title：mSystems

authors： Wang Y,Wang S,Wu C,Chen X,Duan Z,Xu Q,Jiang W,Xu L,Wang T,Su L,Wang Y,Chen Y,Zhang J,Huang Y,Tong S,Zhou C,Deng S,Qin N

更新日期：2019-11-05 00:00:00

abstract：:Microbial and plant specialized metabolites, also known as natural products, are key mediators of microbe-microbe and host-microbe interactions and constitute a rich resource for drug development. In the past decade, genome mining has emerged as a prominent strategy for natural product discovery. Initially, such minin...

journal_title：mSystems

authors： Medema MH

更新日期：2018-03-06 00:00:00

abstract：:Nutrient acquisition from the host environment is crucial for the survival of intracellular pathogens, but conceptual and technical challenges limit our knowledge of pathogen diets. To overcome some of these technical roadblocks, we exploited an experimentally accessible model for early infection of human macrophages ...

journal_title：mSystems

authors： Zimmermann M,Kogadeeva M,Gengenbacher M,McEwen G,Mollenkopf HJ,Zamboni N,Kaufmann SHE,Sauer U

更新日期：2017-08-22 00:00:00

abstract：:GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a dat...

journal_title：mSystems

authors： Price MN,Deutschbauer AM,Arkin AP

更新日期：2020-06-23 00:00:00

abstract：:The intestinal microbiota and the expanded endocannabinoid (eCB) system, or endocannabinoidome (eCBome), have both been implicated in diet-induced obesity and dysmetabolism. These systems were recently suggested to interact during the development of obesity. We aimed at identifying the potential interactions between g...

journal_title：mSystems

authors： Lacroix S,Pechereau F,Leblanc N,Boubertakh B,Houde A,Martin C,Flamand N,Silvestri C,Raymond F,Di Marzo V,Veilleux A

更新日期：2019-12-17 00:00:00

abstract：:Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have been identified as the...

journal_title：mSystems

authors： Brooks LE,Ul-Hasan S,Chan BK,Sistrom MJ

更新日期：2018-04-17 00:00:00

abstract：:Classified as a biosafety level 4 (BSL4) select agent, Nipah virus (NiV) is a deadly henipavirus in the Paramyxoviridae family, with a nearly 75% mortality rate in humans, underscoring its global and animal health importance. Elucidating the process of viral particle production in host cells is imperative both for tar...

journal_title：mSystems

authors： Johnston GP,Bradel-Tretheway B,Piehowski PD,Brewer HM,Lee BNR,Usher NT,Zamora JLR,Ortega V,Contreras EM,Teuton JR,Wendler JP,Matz KM,Adkins JN,Aguilar HC

更新日期：2019-09-24 00:00:00

abstract：:It is important to expedite our understanding of antibiotic resistance to address the increasing numbers of fatalities and environmental pollution due to the emergence of antibiotic resistance and multidrug-resistant strains. Here, we combined the CRISPR-enabled trackable genome engineering (CREATE) technology and tra...

journal_title：mSystems

authors： Chen C,Choudhury A,Zhang S,Garst AD,Song X,Liu X,Chen T,Gill RT,Wang Z

更新日期：2020-04-21 00:00:00