15 research outputs found
Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens
Conservation and Diversity of Seed Associated Endophytes in Zea across Boundaries of Evolution, Ethnography and Ecology
Endophytes are non-pathogenic microbes living inside plants. We asked whether endophytic species were conserved in the agriculturally important plant genus Zea as it became domesticated from its wild ancestors (teosinte) to modern maize (corn) and moved from Mexico to Canada. Kernels from populations of four different teosintes and 10 different maize varieties were screened for endophytic bacteria by culturing, cloning and DNA fingerprinting using terminal restriction fragment length polymorphism (TRFLP) of 16S rDNA. Principle component analysis of TRFLP data showed that seed endophyte community composition varied in relation to plant host phylogeny. However, there was a core microbiota of endophytes that was conserved in Zea seeds across boundaries of evolution, ethnography and ecology. The majority of seed endophytes in the wild ancestor persist today in domesticated maize, though ancient selection against the hard fruitcase surrounding seeds may have altered the abundance of endophytes. Four TRFLP signals including two predicted to represent Clostridium and Paenibacillus species were conserved across all Zea genotypes, while culturing showed that Enterobacter, Methylobacteria, Pantoea and Pseudomonas species were widespread, with γ-proteobacteria being the prevalent class. Twenty-six different genera were cultured, and these were evaluated for their ability to stimulate plant growth, grow on nitrogen-free media, solubilize phosphate, sequester iron, secrete RNAse, antagonize pathogens, catabolize the precursor of ethylene, produce auxin and acetoin/butanediol. Of these traits, phosphate solubilization and production of acetoin/butanediol were the most commonly observed. An isolate from the giant Mexican landrace Mixteco, with 100% identity to Burkholderia phytofirmans, significantly promoted shoot potato biomass. GFP tagging and maize stem injection confirmed that several seed endophytes could spread systemically through the plant. One seed isolate, Enterobacter asburiae, was able to exit the root and colonize the rhizosphere. Conservation and diversity in Zea-microbe relationships are discussed in the context of ecology, crop domestication, selection and migration
4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?
Abrupt Temporal Fluctuations in the Chicken Fecal Microbiota Are Explained by Its Gastrointestinal Origin
Assessment of the Geographic Origins of Pinewood Nematode Isolates via Single Nucleotide Polymorphism in Effector Genes
The pinewood nematode, Bursaphelenchus xylophilus, is native to North America but it only causes damaging pine wilt
disease in those regions of the world where it has been introduced. The accurate detection of the species and its dispersal
routes are thus essential to define effective control measures. The main goals of this study were to analyse the genetic
diversity among B. xylophilus isolates from different geographic locations and identify single nucleotide polymorphism
(SNPs) markers for geographic origin, through a comparative transcriptomic approach. The transcriptomes of seven B.
xylophilus isolates, from Continental Portugal (4), China (1), Japan (1) and USA (1), were sequenced in the next generation
platform Roche 454. Analysis of effector gene transcripts revealed inter-isolate nucleotide diversity that was validated by
Sanger sequencing in the genomic DNA of the seven isolates and eight additional isolates from different geographic
locations: Madeira Island (2), China (1), USA (1), Japan (2) and South Korea (2). The analysis identified 136 polymorphic
positions in 10 effector transcripts. Pairwise comparison of the 136 SNPs through Neighbor-Joining and the Maximum
Likelihood methods and 5-mer frequency analysis with the alignment-independent bilinear multivariate modelling
approach correlated the SNPs with the isolates geographic origin. Furthermore, the SNP analysis indicated a closer proximity
of the Portuguese isolates to the Korean and Chinese isolates than to the Japanese or American isolates. Each geographic
cluster carried exclusive alleles that can be used as SNP markers for B. xylophilus isolate identification
“What She Told Us Made the world of Difference”: Carers’ Perspectives on A Hospice at Home Service
Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing
Variations of Phosphorous Accessibility Causing Changes in Microbiome Functions in the Gastrointestinal Tract of Chickens
Characterization of Egg Laying Hen and Broiler Fecal Microbiota in Poultry Farms in Croatia, Czech Republic, Hungary and Slovenia
Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach
The potential presence of widespread and stable bacterial core phylogroups in the human colon has promoted considerable attention. Despite major efforts, no such phylogroups have yet been identified. Therefore, using a novel phylogroup- and tree-independent approach, we present a reanalysis of 1 114 722 V2 region and 71 550 near full-length 16S rRNA sequences from a total of 210 human beings, with widespread geographic origin, ethnic background and diet, in addition to a wide range of other mammals. We found two highly prevalent core phylogroups (cores 1 and 2), belonging to the clostridial family Lachnospiraceae. These core phylogroups showed a log-normal distribution among human individuals, while non-core phylogroups showed more skewed distributions towards individuals with low levels compared with the log-normal distribution. Molecular clock analyses suggest that core 2 co-evolved with the radiation of vertebrates, while core 1 co-evolved with the mammals. Taken together, the stability, prevalence and potential functionality support the fact that the identified core phylogroups are pivotal in maintaining gut homeostasis and health