BSGatlas : a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access

A large part of our current understanding of gene regulation in Gram-positive bacteria is based on Bacillus subtilis , as it is one of the most well studied bacterial model systems. The rapid growth in data concerning its molecular and genomic biology is distributed across multiple annotation resources. Consequently, the interpretation of data from further B. subtilis experiments becomes increasingly challenging in both low- and large-scale analyses. Additionally, B. subtilis annotation of structured RNA and non-coding RNA (ncRNA), as well as the operon structure, is still lagging behind the annotation of the coding sequences. To address these challenges, we created the B. subtilis genome atlas, BSGatlas, which integrates and unifies multiple existing annotation resources. Compared to any of the individual resources, the BSGatlas contains twice as many ncRNAs, while improving the positional annotation for 70 % of the ncRNAs. Furthermore, we combined known transcription start and termination sites with lists of known co-transcribed gene sets to create a comprehensive transcript map. The combination with transcription start/termination site annotations resulted in 717 new sets of co-transcribed genes and 5335 untranslated regions (UTRs). In comparison to existing resources, the number of 5′ and 3′ UTRs increased nearly fivefold, and the number of internal UTRs doubled. The transcript map is organized in 2266 operons, which provides transcriptional annotation for 92 % of all genes in the genome compared to the at most 82 % by previous resources. We predicted an off-target-aware genome-wide library of CRISPR–Cas9 guide RNAs, which we also linked to polycistronic operons. We provide the BSGatlas in multiple forms: as a website (https://rth.dk/resources/bsgatlas/), an annotation hub for display in the UCSC genome browser, supplementary tables and standardized GFF3 format, which can be used in large scale -omics studies. By complementing existing resources, the BSGatlas supports analyses of the B. subtilis genome and its molecular biology with respect to not only non-coding genes but also genome-wide transcriptional relationships of all genes

Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota)

Compared to the higher fungi (Dikarya), taxonomic and evolutionary studies on the basal clades of fungi are fewer in number. Thus, the generic boundaries and higher ranks in the basal clades of fungi are poorly known. Recent DNA based taxonomic studies have provided reliable and accurate information. It is therefore necessary to compile all available information since basal clades genera lack updated checklists or outlines. Recently, Tedersoo et al. (MycoKeys 13:1--20, 2016) accepted Aphelidiomycota and Rozellomycota in Fungal clade. Thus, we regard both these phyla as members in Kingdom Fungi. We accept 16 phyla in basal clades viz. Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. Thus, 611 genera in 153 families, 43 orders and 18 classes are provided with details of classification, synonyms, life modes, distribution, recent literature and genomic data. Moreover, Catenariaceae Couch is proposed to be conserved, Cladochytriales Mozl.-Standr. is emended and the family Nephridiophagaceae is introduced

Effects of inclusion of microbial cultures in barley-based diets fed to laying hens

The effect of a mix of freeze dried Lactobacillus acidophilus plus Lactobacillus casei (2.3 × 108 colony forming units (cfu) kg-1 feed), or concentrates of Bacillus cereus (CICT-953) (109 cfu kg-1 feed), or Streptococcus faecium (CL-15) (1.5 × 109 cfu kg-1) on laying performance and mineral metabolism in White Leghorn hens was investigated in three 16-week experiments. A maize-barley (50/50) based diet (Experiment 1) or a barley based diet (Experiments 2 and 3) was used. The first experiment involved two treatments: a control diet and the same diet with L. acidophilus plus L. casei mixed culture. Supplementation improved hen day egg production (P<0.01), feed conversion ratio (P<0.01), egg weight (P<0.05) and albumen quality (P<0.05). Feed consumption and egg specific gravity were not influenced by the treatments. The second experiment also involved two treatments: an unsupplemented control diet and the same diet with B. cereus concentrate. Increased (P<0.01) egg weight and albumen quality were observed in hens receiving the B. cereus culture. There were no significant differences in feed consumption, feed conversion ratio or egg specific gravity. The third experiment involved four dietary treatments: control diet; control diet with L. acidophilus plus L. casei mixed culture; control diet with B. cereus concentrate; or control diet with S. faecium concentrate. The L. acidophilus plus L. casei mix improved hen day egg production (P<0.01), egg weight (P<0.05), and albumen quality (P<0.01). Feed consumption and feed conversion ratio were not affected by the addition of lactobacilli to the diet. Supplementation of B. cereus to the diet determined similar response to that indicated in Experiment 2. Birds receiving S. faecium produced greater egg mass (P<0.01), egg weight (P<0.01) and albumen quality (P<0.01). Feed consumption, feed conversion ratio and egg specific gravity did not differ from the control group. Although calcium retention was not significantly affected by feeding the microorganisms cultures, it tended to improve by 2.4-4.2%. Addition of bacterial cultures to barley diet increased (P<0.01) shell calcium. Plasma calcium, phosphorus, magnesium and zinc levels were similar to those of hens on the control diet. Feeding the S. faecium culture decreased (P<0.05) serum copper. Laying hens fed an L. acidophilus plus L. casei mixed culture showed a decrease in serum iron (P<0.01). © 1995.Peer Reviewe

Utilización biológica de distintas fuentes de Zn en los broilers

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The influence of intestinal (Ceca) flora on serum and egg yolk cholesterol levels in laying hens

Normal and cecectomized laying hens were used to study the influence of intestinal (ceca) flora and the implantation of Lactobacillus acidophylus on the levels of serum and egg yolk cholesterol. The ceca had been surgically removed when the experimental birds were 16 months of age. Serum cholesterol levels of cecectomized laying hens were higher than that of normal birds; the Lactobacillus acidophylus implantation resulted in a significant decrease in serum cholesterol levels in both normal and cecectomized birds. The normal intestinal (ceca) flora and Lactobacillus acidophylus implantation did not influence fat digestibility. Egg yolk cholesterol levels were higher for cecectomized birds. A constant relationship between serum and egg yolk cholesterol was not observed.This work was supported in part by the Instituto de Microbiologia Industrial.Peer reviewe