Abstract:
:Plant polysaccharide breakdown by microbes in the rumen is fundamental to digestion in ruminant livestock. Bacterial species belonging to the rumen genera Butyrivibrio and Pseudobutyrivibrio are important degraders and utilizers of lignocellulosic plant material. These bacteria degrade polysaccharides and ferment the released monosaccharides to yield short-chain fatty acids that are used by the ruminant for growth and the production of meat, milk, and fiber products. Although rumen Butyrivibrio and Pseudobutyrivibrio species are regarded as common rumen inhabitants, their polysaccharide-degrading and carbohydrate-utilizing enzymes are not well understood. In this study, we analyzed the genomes of 40 Butyrivibrio and 6 Pseudobutyrivibrio strains isolated from the plant-adherent fraction of New Zealand dairy cows to explore the polysaccharide-degrading potential of these important rumen bacteria. Comparative genome analyses combined with phylogenetic analysis of their 16S rRNA genes and short-chain fatty acid production patterns provide insight into the genomic diversity and physiology of these bacteria and divide Butyrivibrio into 3 species clusters. Rumen Butyrivibrio bacteria were found to encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) and binding proteins. In total, 4,421 glycoside hydrolases (GHs), 1,283 carbohydrate esterases (CEs), 110 polysaccharide lyases (PLs), 3,605 glycosyltransferases (GTs), and 1,706 carbohydrate-binding protein modules (CBM) with predicted activities involved in the depolymerization and transport of the insoluble plant polysaccharides were identified. Butyrivibrio genomes had similar patterns of CAZyme families but varied greatly in the number of genes within each category in the Carbohydrate-Active Enzymes database (CAZy), suggesting some level of functional redundancy. These results suggest that rumen Butyrivibrio species occupy similar niches but apply different degradation strategies to be able to coexist in the rumen.IMPORTANCE Feeding a global population of 8 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. Members of the genera Butyrivibrio and Pseudobutyrivibrio are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings have highlighted the immense enzymatic machinery of Butyrivibrio and Pseudobutyrivibrio species for the degradation of plant fiber, suggesting that these bacteria occupy similar niches but apply different degradation strategies in order to coexist in the competitive rumen environment.
journal_name
Appl Environ Microbioljournal_title
Applied and environmental microbiologyauthors
Palevich N,Kelly WJ,Leahy SC,Denman S,Altermann E,Rakonjac J,Attwood GTdoi
10.1128/AEM.01993-19subject
Has Abstractpub_date
2019-12-13 00:00:00issue
1eissn
0099-2240issn
1098-5336pii
AEM.01993-19journal_volume
86pub_type
杂志文章abstract::The reliable detection of airborne biological threat agents depends on several factors, including the performance criteria of the detector and its operational environment. One step in improving the detector's performance is to increase our knowledge of the biological aerosol background in potential operational environ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.07212-11
更新日期:2012-03-01 00:00:00
abstract::Seven different sources of inocula that included sediments, contaminated soils, groundwater, process effluent, and sludge were used to establish enrichment cultures of denitrifying bacteria on benzene, toluene, and xylenes in the absence of molecular oxygen. All of the enrichment cultures demonstrated complete depleti...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.57.2.450-454.1991
更新日期:1991-02-01 00:00:00
abstract::A molecular diagnostic system using single nucleotide polymorphisms (SNPs) was developed to identify four Sclerotinia species: S. sclerotiorum (Lib.) de Bary, S. minor Jagger, S. trifoliorum Erikss., and the undescribed species Sclerotinia species 1. DNAs of samples are hybridized with each of five 15-bp oligonucleoti...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.02761-08
更新日期:2009-09-01 00:00:00
abstract::A total of 896 samples of retail fresh meats and poultry was assayed for Escherichia coli serogroup O157:H7 by a hydrophobic grid membrane filter-immunoblot procedure developed specifically to isolate the organism from foods. The procedure involves several steps, including selective enrichment, filtration of enrichmen...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.53.10.2394-2396.1987
更新日期:1987-10-01 00:00:00
abstract::The wood decay basidiomycete Phanerochaete chrysosporium was grown under standard ligninolytic or cellulolytic conditions and subjected to whole-genome expression microarray analysis and liquid chromatography-tandem mass spectrometry of extracellular proteins. A total of 545 genes were flagged on the basis of signific...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00314-09
更新日期:2009-06-01 00:00:00
abstract::A mutant (furA3) was isolated from the S1 wild-type strain of Nectria haematococca on the basis of its resistance to 5-fluorouracil (5FU). This mutant has greatly reduced activity of uracil phosphoribosyltransferase, a pyrimidine salvage enzyme catalyzing the synthesis of UMP from uracil. The metabolism of 5FU was exa...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.55.10.2474-2479.1989
更新日期:1989-10-01 00:00:00
abstract::A new genus and species of a nonmotile gram-negative rod, Syntrophobacter wolinii, is the first bacterium described which degrades propionate only in coculture with an H(2)-using organism and in the absence of light or exogenous electron acceptors such as O(2), sulfate, or nitrate. It was isolated from methanogenic en...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.40.3.626-632.1980
更新日期:1980-09-01 00:00:00
abstract::Environmental contamination with compounds containing oxyanions of chlorine, such as perchlorate or chlorate [(per)chlorate] or chlorine dioxide, has been a constantly growing problem over the last 100 years. Although the fact that microbes reduce these compounds has been recognized for more than 50 years, only six or...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.65.12.5234-5241.1999
更新日期:1999-12-01 00:00:00
abstract::Strain DCB-1 is an obligately anaerobic bacterium which carries out the reductive dehalogenation of halobenzoates and was previously known to grow only on pyruvate plus 20% ruminal fluid. When various electron acceptors were supplied, thiosulfate and sulfite were found to stimulate growth. Sulfide was produced from th...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.54.12.2938-2943.1988
更新日期:1988-12-01 00:00:00
abstract::Located in southwest China, the Aha watershed is continually contaminated by acid mine drainage (AMD) produced from upstream abandoned coal mines. The watershed is fed by creeks with elevated concentrations of aqueous Fe (total Fe > 1 g/liter) and SO4 (2-) (>6 g/liter). AMD contamination gradually decreases throughout...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00935-15
更新日期:2015-08-01 00:00:00
abstract::The cry19A operon of Bacillus thuringiensis subsp. jegathesan encodes two proteins, mosquitocidal Cry19A (ORF1; 75 kDa) and an ORF2 (60 kDa) of unknown function. Expression of the cry19A operon in an acrystalliferous strain of B. thuringiensis (4Q7) yielded one small crystal per cell, whereas no crystals were produced...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.06750-11
更新日期:2012-03-01 00:00:00
abstract::An efficient method for the transformation of the methylotrophic bacterium Methylobacterium extorquens NR-2 with a broad-host-range plasmid, pLA2917, by electroporation was examined. Transformants of M. extorquens NR-2 expressing resistance to kanamycin were obtained after electric pulse. These transformants were foun...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.57.4.924-926.1991
更新日期:1991-04-01 00:00:00
abstract::In in vitro estuarine water and sediment chambers, the survival of Vibrio cholerae and Escherichia coli was determined by plate counting and direct counting techniques. V. cholerae strains included environmental, clinical, and serotype O1 and non-O1 isolates, whereas E. coli strains included ATCC 25922 and a freshly c...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.43.3.578-584.1982
更新日期:1982-03-01 00:00:00
abstract::Pseudomonas sp. strain ADP uses the herbicide atrazine as the sole nitrogen source. We have devised a simple atrazine degradation assay to determine the effect of other nitrogen sources on the atrazine degradation pathway. The atrazine degradation rate was greatly decreased in cells grown on nitrogen sources that supp...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/aem.69.12.6987-6993.2003
更新日期:2003-12-01 00:00:00
abstract::PCR-based methods have been developed to rapidly screen for Legionella pneumophila in water as an alternative to time-consuming culture techniques. However, these methods fail to discriminate between live and dead bacteria. Here, we report a viability assay (viability PCR [v-PCR]) for L. pneumophila that combines ethi...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.02878-08
更新日期:2009-06-01 00:00:00
abstract::A fixed-bed loop, high-rate anaerobic bioreactor treating sulfite evaporator condensate was sampled when it reached steady state and afterwards following perturbations during a 14-month period. By using immunotechnology, it was observed that shifts in methanogenic subpopulations occurred in association with perturbati...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.55.8.1996-2001.1989
更新日期:1989-08-01 00:00:00
abstract::Resistance to HIV infection in a cohort of commercial sex workers living in Nairobi, Kenya, is linked to mucosal and antiinflammatory factors that may be influenced by the vaginal microbiota. Since bacterial vaginosis (BV), a polymicrobial dysbiosis characterized by low levels of protective Lactobacillus organisms, is...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.02943-10
更新日期:2011-06-01 00:00:00
abstract::Pediocin PA-1 is an antimicrobial peptide (called bacteriocin) that shows inhibitory activity against the food-borne pathogen Listeria monocytogenes. To elucidate which residue(s) is responsible for this function, the antimicrobial activities of pediocin PA-1 mutants were evaluated and compared. Each of the 44 native ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.72.2.1141-1147.2006
更新日期:2006-02-01 00:00:00
abstract::Fifteen Bacillus thuringiensis strains representing 13 serotypes were screened with five oligodeoxyribonucleotide probes specific for certain regions of two published sequences and one unpublished sequence of B. thuringiensis delta-endotoxin genes. Of the 15 cultures, 14 hybridized with at least one probe; the B. thur...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.53.12.2808-2814.1987
更新日期:1987-12-01 00:00:00
abstract::Dehalobacter and "Dehalococcoides" spp. were previously shown to be involved in the biotransformation of 1,1,2-trichloroethane (1,1,2-TCA) and 1,2-dichloroethane (1,2-DCA) to ethene in a mixed anaerobic enrichment culture. Here we report the further enrichment and characterization of a Dehalobacter sp. from this mixed...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.02037-08
更新日期:2009-05-01 00:00:00
abstract::Aeromonas sp. will methylate trimethyl lead acetate (Me3PbOAc) to volatile tetramethyl lead (Me4Pb). Examination of cultures grown in the presence of Me3PbOAc revealed no major irregularities between cells of the treated and untreated cultures. Some cells, however, showed evidence that intracytoplasmic materials had b...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.32.5.723-725.1976
更新日期:1976-11-01 00:00:00
abstract::Our previous genetic analysis (J. W. Willis, J. K. Engwall, and A. K. Chatterjee, Phytopathology 77:1199-1205, 1987) had revealed a tight linkage between pel-3 (pel, pectate lyase gene) and peh-1 (peh, polygalacturonase gene) within the chromosome of Erwinia carotovora subsp. carotovora 71. Nucleotide sequencing, tran...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.60.7.2545-2552.1994
更新日期:1994-07-01 00:00:00
abstract::A compact housing unit for low-power (X6 to X50) cinemicrographic studies of microbial specimens in the vertical plane is described. This unit was used successfully to record the development of a "halo" of cells around subsurface colonies of Escherichia coli. ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.32.2.294-297.1976
更新日期:1976-08-01 00:00:00
abstract::Two constructs derived from the alpha-amylase gene (amyA) of Lactobacillus amylovorus were expressed in Lactobacillus plantarum, and their expression products were purified, characterized, and compared. These products correspond to the complete (AmyA) and truncated (AmyADelta) forms of alpha-amylase; AmyADelta lacks t...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/aem.66.8.3350-3356.2000
更新日期:2000-08-01 00:00:00
abstract::Most associations between animals and their gut microbiota are dynamic, involving sustained transfer of food-associated microbial cells into the gut and shedding of microorganisms into the external environment with feces, but the interacting effects of host and microbial factors on the composition of the internal and ...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01442-15
更新日期:2015-09-01 00:00:00
abstract::Peanut kernels (Tainan 9, a Spanish cultivar) inoculated with Aspergillus parasiticus, A. flavus, A. niger, or A. ochraceus as well as noninoculated kernels were incubated in a humidified environment (relative humidity, 100%) at 25(deg)C for 7 weeks. Internal fungal populations and changes in moisture and sucrose cont...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.63.3.1083-1087.1997
更新日期:1997-03-01 00:00:00
abstract::Maltose-limited, continuous growth of the hyperthermophile Thermotoga maritima at different temperatures and dilution rates (80 degrees C/0.25 h(-1), 80 degrees C/0.17 h(-1), and 85 degrees C/0.25 h(-1)) showed that transcriptome-wide variation in gene expression within mechanical steady states was minimal compared to...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.71.9.5572-5576.2005
更新日期:2005-09-01 00:00:00
abstract::A new bacterial xylanase belonging to family 5 of glycosyl hydrolases was identified and characterized. The xylanase, Xyn5B from Bacillus sp. strain BP-7, was active on neutral, nonsubstituted xylooligosaccharides, showing a clear difference from other GH5 xylanases characterized to date that show a requirement for me...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.00871-10
更新日期:2010-09-01 00:00:00
abstract::The ability of bifidobacteria to adhere to the intestine of the human host is considered to be important for efficient colonization and achieving probiotic effects. Bifidobacterium bifidum strains DSM20456 and MIMBb75 adhere well to the human intestinal cell lines Caco-2 and HT-29. The surface lipoprotein BopA was pre...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.01993-13
更新日期:2013-11-01 00:00:00
abstract::An enrichment method using d-cycloserine was designed for the isolation of spontaneous mutants of Zymomonas mobilis deficient in glucose or fructose utilization. The mutants could easily be isolated since they represented 80 to 90% of the population after two and three enrichment cycles. Glucokinase and fructokinase a...
journal_title:Applied and environmental microbiology
pub_type: 杂志文章
doi:10.1128/AEM.62.3.1096-1098.1996
更新日期:1996-03-01 00:00:00