Abstract:
:This study investigated the impacts of bacterial DNA extraction methodology on downstream analysis of fish gut microbiota. Feces and intestine samples were taken from three sympatric freshwater fish species with varying diets. Samples were processed immediately (approximately 4 h after capture; fresh), stored at -20 °C for 15 days or preserved in RNAlater® reagent for 15 days. DNA was then extracted using two commercial kits: one designed for animal tissues and one specifically formulated for stool samples. Microbial community fingerprints were generated using ribosomal intergenic spacer analysis. Factors including diversity as depicted by band number, band intensity, repeatability and practicalities such as cost and time were considered. Despite significant differences in microbiota structure, results were similar between feces and intestine samples. Frozen samples were consistently outperformed by other storage methods and the stool kit typically outperformed the tissue kit. Overall, we recommend extraction of bacterial DNA from fresh samples using the stool kit for both sample types. If samples cannot be processed immediately, preservation in RNAlater® is preferred to freezing. Choice of DNA extraction method significantly influences the results of downstream microbial community analysis and thus should be taken into consideration for metadata analysis.
journal_name
FEMS Microbiol Lettjournal_title
FEMS microbiology lettersauthors
Larsen AM,Mohammed HH,Arias CRdoi
10.1093/femsle/fnu031subject
Has Abstractpub_date
2015-03-01 00:00:00issue
5eissn
0378-1097issn
1574-6968pii
fnu031journal_volume
362pub_type
杂志文章abstract::Defects in the acd gene (which may be allelic to ubiH) result in the inactivation of the coenzyme A-linked acetaldehyde dehydrogenase activity of the multifunctional AdhE protein of Escherichia coli. This activity is restored by addition of ubiquinone-0 to cell extracts. However, the alcohol dehydrogenase activity of ...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2000.tb08872.x
更新日期:2000-01-01 00:00:00
abstract::The identification of virulence factors in Rhodococcus equi has been severely hampered by the lack of a method for in vivo random insertion mutagenesis. This study reports the use of transposomes to generate random insertions of a gene conferring kanamycin resistance into the genome of R. equi ATCC 33701. Southern hyb...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2001.tb10955.x
更新日期:2001-12-18 00:00:00
abstract::We report for the first time the production of acyl homoserine lactones (AHLs) by Erwina amylovora, an important quarantine bacterial pathogen that causes fire blight in plants. E. amylovora produces one N-acyl homoserine lactone [a N-(3-oxo-hexanoyl)-homoserine lactone or a N-(3-hydroxy-hexanoyl)-homoserine lactone] ...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1016/j.femsle.2004.10.015
更新日期:2004-12-15 00:00:00
abstract::A Phoma sp. was isolated and characterized as endophytic and as a pathogen of Larrea tridentata (creosote bush) growing in the desert region of southern Utah, USA. This fungus produces a unique mixture of volatile organic compounds (VOCs), including a series of sesquiterpenoids, some alcohols and several reduced napht...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2011.02297.x
更新日期:2011-07-01 00:00:00
abstract::Academic work at different career stages has changed and a broadened portfolio of expertise enables academics to adapt, maintain and advance their career. Development related to research activity is naturally driven by methodology and technology. Institutions and peers largely support development in the contexts of di...
journal_title:FEMS microbiology letters
pub_type: 杂志文章,评审
doi:10.1093/femsle/fnv156
更新日期:2015-10-01 00:00:00
abstract::The mosquitocidal crystal protein, Cry19Aa, from Bacillus thuringiensis ssp. jegathesan, has high toxicity to Anopheles stephensi and Culex pipiens but is less toxic to Aedes aegypti. To study the functional role of putative domain II and surface residues in mosquito toxicity, 16 alanine substitution mutations were in...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2009.01583.x
更新日期:2009-06-01 00:00:00
abstract::Vibrio cholerae non-O1 strain N037 produced a hemolysin (NO37-Hly) which was antigenically similar to E1 Tor hemolysin (E1 Tor-Hly) but different in molecular size, hemolytic activity, and glucose binding capacity. In the gene encoding NO37-Hly, a 4-bp insertion into the structural gene for E1 Tor-Hly (hlyA) was found...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.1995.tb07876.x
更新日期:1995-11-01 00:00:00
abstract::This communication presents experimental evidence that intact fragile (osmotic sensitive) yeasts can be electrofused and give viable hybrids. The yield increases with one order of magnitude for electrofusion of intact fragile yeasts with protoplasts of non-fragile ones. The yield of viable hybrids, obtained by electro...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1016/0378-1097(89)90078-5
更新日期:1989-07-01 00:00:00
abstract::The role in virulence of Actinobacillus pleuropneumoniae urease activity was investigated. A urease-negative mutant was isolated following transposon mutagenesis with a mini-Tn10 derivative. Both the parent strain and the urease-negative mutant exhibited identical LD50 values in a murine infection model. Pig challenge...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.1997.tb10266.x
更新日期:1997-03-01 00:00:00
abstract::The filamentous fungus Fusarium lateritium is cyanide tolerant, due partly to the induction of the enzyme cyanide hydratase in the presence of cyanide. This enzyme catalyses the hydration of cyanide to formamide. The expression in Escherichia coli of a cDNA clone encoding cyanide hydratase is described. The cDNA clone...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.1995.tb07928.x
更新日期:1995-12-15 00:00:00
abstract::The presence of insertion sequence IS1 in 70 multiple-antibiotic resistant clinical strains was determined. This 70-strain collection comprised 46 Escherichia coli, 18 Salmonella and 6 Shigella strains. The presence of IS1 was detected in the chromosome and plasmids of 73% and 63% of the strains, respectively, and 51%...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1016/0378-1097(92)90527-u
更新日期:1992-06-01 00:00:00
abstract::A new type II restriction endonuclease, SshAI, was purified from Salmonella shikmonah TK139 of kangaroo origin. The recognition and cleavage specificity of Ssh AI was determined to be 5'-CC/TNAGG-3', identical to that of SauI from Streptomyces aureofaciens and Bsu36I from Bacillus subtilis. Based on closely related an...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1016/0378-1097(90)90291-w
更新日期:1990-01-01 00:00:00
abstract::The 0104 antigen (lipopolysaccharide, LPS) of Escherichia coli has an acidic O specific polysaccharide. From the aqueous phase of a phenol water extraction of E. coli O104: K-, a fraction was obtained by ultracentrifugation and Cetavlon precipitation of the supernatant, which was enriched in long-chain LPS. Compositio...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1016/0378-1097(92)90673-c
更新日期:1992-03-01 00:00:00
abstract::Development of pili on cells of Arthrobacter photogonimos is induced by photo-oxidative conditions. The nucleotide sequence was determined of a light-inducible gene (lipA) that encodes the precursor of a light-inducible pilin (designated LIP), a polypeptide of 212 amino acids. The N-terminal leader peptide includes a ...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.1998.tb13030.x
更新日期:1998-06-01 00:00:00
abstract::We have investigated the iron-dependent regulation of the psbA gene, encoding the enzyme L-ornithine N(5)-oxygenase in the rhizobacterium Pseudomonas B10. We have cloned and characterized a Pseudomonas B10 gene, designated psbS, required for psbA expression. PsbS is endowed with structural and functional features of e...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2002.tb11085.x
更新日期:2002-03-05 00:00:00
abstract::Fusobacterium nucleatum is a common oral anaerobe associated with gingivitis, periodontal disease and preterm deliveries. Coaggregation among oral bacteria is considered to be a significant factor in dental plaque development. Adhesion to host cells was suggested to be important for the F. nucleatum virulence associat...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1016/j.femsle.2005.05.055
更新日期:2005-07-15 00:00:00
abstract::Streptococcus suis serotype 2 (S. suis 2 or SS2) is the causative agent of several diseases in both pigs and humans. 6-Phosphogluconate dehydrogenase (6PGD) is a cell surface protein in SS2. In this study, the immunogenicity and protective efficacy of recombinant 6PGD (r6PGD) from SS2 was evaluated in piglets. Immuniz...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2009.01617.x
更新日期:2009-07-01 00:00:00
abstract::The physiological role of mitochondrial aldehyde dehydrogenase (ALD5) was investigated by analysis of the ald5 mutant (AKD321) in Saccharomyces cerevisiae. K(+)-activated ALDH activity of the ald5 mutant was about 80% of the wild-type in the mitochondrial fraction, while the respiratory activity of the ald5 mutant was...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.1999.tb08856.x
更新日期:1999-12-15 00:00:00
abstract::The amino acid composition and structure of the peptidoglycan from Heliobacillus mobilis was determined by one- and two-dimensional thin-layer chromatography of completely and partially hydrolysed cell wall preparations. The structure was found to be of the A3 gamma type, with L,L-diaminopimelate in position 3, D-alan...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.1994.tb07135.x
更新日期:1994-09-15 00:00:00
abstract::Bordetella pertussis is the causative agent of whooping cough. Traditional vaccines against this disease are inherently reactogenic, thus research is currently focussed on the production of less reactive, acellular vaccines. Expression of candidate antigens for these vaccines in Escherichia coli would be preferable, h...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2000.tb09336.x
更新日期:2000-10-15 00:00:00
abstract::Agrobacterium tumefaciens strain SCUEC1 is a nicotine-degrading bacterium, which has been recently isolated from the tobacco waste-contaminated field soil. However, the mechanism for nicotine degradation in this strain remains unclear. Here, we analyze the function and biological properties of the agnH gene in the str...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1093/femsle/fnaa040
更新日期:2020-02-01 00:00:00
abstract::SPC(3) is a multiple antigen peptide derived from the V(3) loop of human immunodeficiency virus (HIV) envelope (Env). It exerts a potent anti-HIV activity whereas it alters neither Env expression nor binding to CD(4). Here, SPC(3) binding characteristics, its subsequent intracellular fate and the fact that it inhibite...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2000.tb08964.x
更新日期:2000-02-15 00:00:00
abstract::We devised a screening method to obtain basidiomycetous fungi capable of degrading dioxins. About 200 fungal strains were selected from more than 1500 strains by their ability to decolorize Remazol brilliant blue R dye as an indicator. To attempt to eliminate the factor of dioxin sorption by mycelia, we prepared two s...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2002.tb11308.x
更新日期:2002-08-06 00:00:00
abstract::Fourteen solvent-sensitive transposon mutants were generated from the solvent-tolerant Pseudomonas putida strain S12 by applying the TnMod-KmO mutagenesis system. These mutants were unable to grow in the presence of octanol and toluene. By cloning the region flanking the transposon insertion point a partial sequence o...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2001.tb10628.x
更新日期:2001-05-01 00:00:00
abstract::Salmonella enteritidis isolated from poultry infections generated a convoluted colonial morphology after 48 h growth on colonisation factor antigen (CFA) agar at 25 degrees C. A mutant S. enteritidis defective for the elaboration of the SEF17 fimbrial antigen, in which the agf gene cluster was inactivated by insertion...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.1997.tb10460.x
更新日期:1997-08-01 00:00:00
abstract::Mathematical modeling is an important tool in biological research, allowing for the synthesis of results from many studies into an understanding of a system. Despite this, the need for extensive subject matter knowledge and complex mathematics often leaves modeling as an esoteric subspecialty. A 2-fold approach can be...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1093/femsle/fnw225
更新日期:2016-10-01 00:00:00
abstract::During the establishment of Escherichia coli O157:H7 infection, its capacity to adhere to host intestinal epithelial cells is the critical first step in pathogenesis. It also has the capability to form biofilms, and because both are surface activities, we sought to gain insight into a potential linkage between biofilm...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.2010.02173.x
更新日期:2011-02-01 00:00:00
abstract::The galE gene of Pasteurella multocida has been isolated by complementing galE-defective mutants of Salmonella typhimurium with a plasmid library of this organism. The complete nucleotide sequence of the P. multocida galE gene consists of 1017 nucleotides, encoding a predicted polypeptide of 339 amino acids. The deduc...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1111/j.1574-6968.1997.tb12661.x
更新日期:1997-09-15 00:00:00
abstract::The miniplasmid profiles of 18 Bacillus thuringiensis strains belonging to 8 different serotypes were determined using an alkaline hydrolysis method for isolation of low molecular mass plasmids. Nearly all the strains contained covalently closed circular (CCC) DNA species ranging from 2 to 5 species per strain and fro...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1016/0378-1097(92)90641-z
更新日期:1992-07-15 00:00:00
abstract::The cea-kil operon of the ColE1 plasmid is negatively regulated by the LexA-repressor and therefore, it is under the control of SOS regulation. We constructed a gene fusion between the cea and lacZ genes. Expression of the translational fusion can be easily detected by monitoring the levels of beta-galactosidase. Sinc...
journal_title:FEMS microbiology letters
pub_type: 杂志文章
doi:10.1016/0378-1097(91)90232-y
更新日期:1991-07-01 00:00:00