Abstract：
:Metagenomic libraries represent subsamples of the total DNA found at a study site and offer unprecedented opportunities to study ecological and functional aspects of microbial communities. To examine the depth of a community sequencing effort, rarefaction analysis of the ribosomal small subunit (SSU/16S/18S) gene in the metagenome is usually performed. The fragmentary, non-overlapping nature of SSU sequences in metagenomic libraries poses a problem for this analysis, however. We introduce a software package - Megraft - that grafts SSU fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.
journal_name
Res Microbioljournal_title
Research in microbiologyauthors
Bengtsson J,Hartmann M,Unterseher M,Vaishampayan P,Abarenkov K,Durso L,Bik EM,Garey JR,Eriksson KM,Nilsson RHdoi
10.1016/j.resmic.2012.07.001subject
Has Abstractpub_date
2012-07-01 00:00:00pages
407-12issue
6-7eissn
0923-2508issn
1769-7123pii
S0923-2508(12)00096-4journal_volume
163pub_type
杂志文章abstract：:OprI, a small outer membrane lipoprotein from Pseudomonas aeruginosa, can be produced in large amounts and anchored at the surface on Escherichia coli cells. A four-time repeated (His-Cys) motif was fused to the C-terminal part of OprI. After induction, E. coli cells harbouring the recombinant oprI gene became more se...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/s0923-2508(01)01263-3
更新日期：2001-11-01 00:00:00
abstract：:The insertion of proteins into membranes generally requires the assistance of membrane proteins. A protein, designated Omp85 in Neisseria meningitidis, was shown to be required for the assembly of bacterial outer-membrane proteins. The protein is essential for the viability of the bacteria and is ubiquitous among Gram...
journal_title：Research in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.resmic.2003.11.007
更新日期：2004-04-01 00:00:00
abstract：:This brief note reports the nucleotide sequences of the second nifH region of Methanobacterium ivanovii and of the two nifH regions of Methanosarcina barkeri 227. In the three cases, nifH is followed by two ORF (open reading frames) similar to ORF105 and ORF128 respectively, which were previously found downstream of M...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/0923-2508(91)90091-n
更新日期：1991-01-01 00:00:00
abstract：:Macroscopic and microscopic measurements of the growth of Trichoderma viride and Rhizopus oligosporus were compared at different values of water activity of the solid medium. The relationship between radial extension rate and hyphal growth rate was found to be dependent on water activity. The observed difference betwe...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/0923-2508(92)90106-x
更新日期：1992-10-01 00:00:00
abstract：:Energy-coupling factor (ECF) transporters mediate the uptake of micronutrients in prokaryotes. They consist of two ATP-binding-cassette family ATPases, a transmembrane coupling protein (T component) and a substrate-binding membrane protein (S component). ECF transporters for Co2+ and Ni2+ ions have one or two addition...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2019.06.007
更新日期：2019-01-01 00:00:00
abstract：:The major 25-kDa outer membrane protein (Omp25) of Brucella abortus was purified and antigenically characterized by use of monoclonal antibodies (mAbs). Purification was achieved from the sodium dodecyl sulphate-insoluble (SDS-I) cell wall (CW) fraction of vaccine strain B. abortus B19 which was shown by use of mAbs t...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/0923-2508(96)81383-0
更新日期：1996-05-01 00:00:00
abstract：:Klebsiella pneumoniae is one of the major Gram-negative bacterial pathogens causing hospital-acquired multidrug-resistant infections, and the antimicrobial treatment options are scarce. The lack of available antimicrobials has prompted the development of alternative strategies for the treatment of these infections. In...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2019.01.003
更新日期：2019-01-01 00:00:00
abstract：:Recent studies suggest that viruses are the most numerous entities in the biosphere; bacteriophages, the viruses that infect Eubacteria and Archaea, constitute a substantial fraction of this population. In spite of their ubiquity, the vast majority of phages in the environment have never been studied and nothing is kn...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/S0923-2508(03)00069-X
更新日期：2003-05-01 00:00:00
abstract：:Bacterial membranes are known to form domains with specific lipid compositions and functions. Recently, using membrane binding fluorescent dyes, lipid spiral structures extending along the long axis of the cell were detected. These spirals were absent when the synthesis of phosphatidylglycerol and cardiolipin was disr...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2010.07.006
更新日期：2010-11-01 00:00:00
abstract：:A variety of pathways for carbon and electron flow in the bacterium Escherichia coli and in other enteric bacteria are differentially expressed depending on whether molecular oxygen is present in the cell environment. This review briefly summarizes the metabolic pathways operative during aerobic versus anaerobic cell ...
journal_title：Research in microbiology
pub_type： 杂志文章,评审
doi：10.1016/0923-2508(94)90092-2
更新日期：1994-06-01 00:00:00
abstract：:By employing flow cytometry, the DNA content and cell size of individual bacterial cells may be determined rapidly and with high precision. Also, the number of DNA replication origins in Escherichia coli cells can be measured after treating the cells with rifampicin together with the cell division inhibitor cephalexin...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/0923-2508(91)90020-b
更新日期：1991-02-01 00:00:00
abstract：:The association between bacteria and leaves in Ardisia has been described as a cyclic and obligate symbiosis in which bacteria are maintained throughout all stages of the plant's life cycle to guarantee normal growth and survival of the host. This intimate interaction suggests that both partners have co-diversified to...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2011.04.003
更新日期：2011-06-01 00:00:00
abstract：:Bacillus subtilis ATCC6633 produces mycosubtilin, a non-ribosomally synthesized lipopeptide of the iturin family which presents antagonistic activities toward various phytopathogens. Different homologues with fatty acid moiety varying from C15 to C17 are usually co-produced, with their biological activities increasing...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2008.05.004
更新日期：2008-07-01 00:00:00
abstract：:Mesophilic iron and sulfur-oxidizing acidophiles are readily found in acid mine drainage sites and bioleaching operations, but relatively little is known about their activities at suboptimal temperatures and in cold environments. The purpose of this work was to characterize the oxidation of elemental sulfur (S(0)), te...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2009.08.022
更新日期：2009-12-01 00:00:00
abstract：:The tricarballylate utilization locus (tcuRABC) of Salmonella enterica serovar Typhimurium is comprised of a 3-gene operon (tcuABC) that encodes functions that allow this bacterium to use tricarballylate as a source of carbon and energy, and the tcuR gene, which encodes a putative LysR-type transcriptional regulator. ...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2009.01.001
更新日期：2009-04-01 00:00:00
abstract：:Translation termination in eukaryotes is mediated by two polypeptide chain-release factors, eRF1 and eRF3. eRF1 recognizes stop signals, while eRF3 is a ribosome-dependent and eRF1-dependent GTPase. eRF1 forms a stable complex with eRF3 in vivo and in vitro. In the present study, a variety of truncated forms of Euplot...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2006.07.005
更新日期：2006-11-01 00:00:00
abstract：:The structure of spiroplasmas in the Chinese mitten crab associated with tremor disease was studied by transmission electron microscopy techniques, including both negative staining and ultrasectioning. A spiral structure, which is a typical form of spiroplasmas, could be detected and the observations showed for the fi...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2004.04.010
更新日期：2004-10-01 00:00:00
abstract：:The biological complexity of trade-offs has been a major obstacle in understanding bacterial diversity and coexistence. Here we reduce the biological complexity by using isogenic Escherichia coli strains differing only in a multiplication-survival trade-off regulated by RpoS. The contribution of trade-off characterist...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2015.12.001
更新日期：2016-04-01 00:00:00
abstract：:A bacteriolytic enzyme excreted by Pseudomonas aeruginosa Paks I was purified: samples were found to be homogeneous by gel filtration chromatography, ion exchange chromatography using CM-cellulose, immunoelectrophoresis, PAGE and SDS-PAGE. The molecular weight of the lytic enzyme was estimated to be 15,000-19,000. The...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/0923-2508(89)90046-6
更新日期：1989-02-01 00:00:00
abstract：:Production of aerobactin has been reported to be a virulence factor in members of the family Enterobacteriaceae. To investigate the protection afforded by humoral immunity directed towards aerobactin in infectious diseases caused by aerobactin-producing strains, we tested the efficacy of mAbAERO1, a murine monoclonal ...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/0923-2508(96)80894-1
更新日期：1995-02-01 00:00:00
abstract：:RNase E is an endoribonuclease and plays a central role in RNA metabolism. Cyanobacteria, as ancient oxygen-producing photosynthetic bacteria, also contain RNase E homologues. Here, we introduced mutations into the S1 subdomain (F53A), the 5'-sensor subdomain (R160A), and the DNase I subdomain (D296A) according to the...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2020.06.001
更新日期：2020-01-01 00:00:00
abstract：:Although it seems obvious that fever has some important general adaptive value, it is still not clear by what means this function is manifested. One postulate is that febrile conditions result in the sequestration of soluble iron, effectively starving some pathogens of that essential nutrient. On the basis of our rece...
journal_title：Research in microbiology
pub_type： 杂志文章,评审
doi：10.1016/0923-2508(94)90182-1
更新日期：1994-05-01 00:00:00
abstract：:Benzene is biodegraded in the absence of oxygen under a variety of terminal electron-accepting conditions. However, the mechanism by which anaerobic benzene degradation occurs is unclear. Phenol and benzoate have been consistently detected as intermediates of anaerobic benzene degradation, suggesting that the hydroxyl...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/s0923-2508(02)01378-5
更新日期：2002-12-01 00:00:00
abstract：:A highly effective chlorpyrifos-degrading bacterium strain Dsp-2 was isolated from the polluted treatment system of a chlorpyrifos manufacturer. This strain was preliminarily identified as Sphingomonas sp. based on its morphological, physiological and biochemical tests as well as 16S rDNA analysis. It utilized chlorpy...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2006.11.007
更新日期：2007-03-01 00:00:00
abstract：:The structure of DspF, a type III secretion system (T3SS) chaperone required for virulence of the fruit tree pathogen Erwinia amylovora, was modeled based on predicted structural homology to characterized T3SS chaperones. This model guided the selection of 11 amino acid residues that were individually mutated to alani...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2010.05.015
更新日期：2010-09-01 00:00:00
abstract：:A hydrogen-producing bacterial strain was newly isolated from a hot spring and identified as Klebsiella oxytoca HP1 by 16S rRNA gene sequence analysis and detection by BioMerieux Vitek. Important parameters, including substrates, starting pH of culture, temperature and oxygen concentration for batch ferment hydrogen p...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/j.resmic.2004.08.004
更新日期：2005-01-01 00:00:00
abstract：:The reproducibility of random amplified polymorphic DNA (RAPD) was tested using two different thermal cyclers and three brands of Taq DNA polymerase. Three different oligonucleotides were used to obtain patterns of amplified fragments from three DNA samples (Escherichia coli, Bacillus subtilis, and Thermococcus littor...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/0923-2508(93)90194-7
更新日期：1993-06-01 00:00:00
abstract：:Three primers derived from the lap gene were used to distinguish Listeria monocytogenes from L.innocua and other Listeria species. L. monocytogenes and L. innocua yielded a PCR product of 600 and 300 bp, respectively, whereas a typical pattern of three amplimers was observed with L. ivanovii, L. seeligeri and L. welsh...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/0923-2508(96)84020-4
更新日期：1996-10-01 00:00:00
abstract：:Although great strides have been made in the development of recombinant attenuated Vibrio cholerae vaccine strains, the task has not been as simple as once imagined. The initial vaccine candidates proved to be unexpectedly reactogenic but further derivatives, such as CVD103-HgR, are well-tolerated, immunogenic and pro...
journal_title：Research in microbiology
pub_type： 杂志文章
doi：10.1016/0923-2508(90)90128-d
更新日期：1990-09-01 00:00:00
abstract：:Although this volume is dedicated to honoring François Jacob, I would like my contribution to broaden the context by recalling the background within which the scientists of those times operated. The specific scientific accomplishments of Jacob will certainly be covered by the other contributors who collaborated with h...
journal_title：Research in microbiology
pub_type： 传,历史文章,杂志文章
doi：10.1016/j.resmic.2014.05.027
更新日期：2014-06-01 00:00:00
