Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this ...premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of
Bos taurus
(cow) and
Bubalus bubalis
(buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90–96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera
Fibrobacter
,
Bacteroides
,
Clostridium
,
Prevotella
and
Ruminococcus
involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.
We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and ...observation metadata. As the number of categories of comparative omics data types (collectively, the "ome-ome") grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses.
The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages.
The BIOM file format and the biom-format project are steps toward reducing the "bioinformatics bottleneck" that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.
Aims: Metagenomic analysis of milk samples collected from Kankrej, Gir (Bos indicus) and crossbred (Bos taurus × B. indicus) cattle harbouring subclinical mastitis was carried out by next‐generation ...sequencing 454 GS‐FLX technology to elucidate the microbial community structure of cattle milk. Methods and Results: Milk samples from Kankrej, Gir and crossbred cattle were subjected to metagenomic profiling by pyrosequencing. The Metagenomic analysis produced 63·07, 11·09 and 7·87 million base pairs (Mb) of sequence data, assembled in 264 798, 56 114 and 36 762 sequences with an average read length of 238, 197 and 214 nucleotides in Kankrej, Gir and crossbred cattle, respectively. Phylogenetic and metabolic profiles by the web‐based tool MG‐RAST revealed that the members of Enterobacteriales were predominant in mastitic milk followed by Pseudomonadales, Bacillales and Lactobacillales. Around 56 different species with varying abundance were detected in the subclinically infected milk. Escherichia coli was found to be the most predominant species in Kankrej and Gir cattle followed by Pseudomonas aeruginosa, Pseudomonas mendocina, Shigella flexneri and Bacillus cereus. In crossbred cattle, Staphylococcus aureus followed by Klebsiella pneumoniae, Staphylococcus epidermidis and E. coli were detected in descending order. Metabolic profiling indicated fluoroquinolones, methicillin, copper, cobalt–zinc–cadmium as the groups of antibiotics and toxic compounds to which the organisms showed resistance. Sequences indicating potential of organisms exhibiting multidrug resistance against antibiotics and resistance to toxic compounds were also present. Interestingly, presence of bacteriophages against Staph. aureus, E. coli, Enterobacter and Yersinia species was also observed. Conclusions: The analysis identified potential infectious organisms in mastitis, resistance of organisms to antibiotics and chemical compounds and the natural resistance potential of dairy cows. Significance and Impact of the Study: The findings of this study may help in formulating strategies for the prevention and treatment of mastitis in dairy animals and consequently in reducing economic losses incurred because of it.
•Development of multigroup advanced semi analytic nodal method solver for HTGR analysis.•Analysis of MHTGR-350 benchmark.•Verification of the developed solver with commercial neutronics codes.
This ...study introduces the multigroup advanced semi-analytic nodal method (A-SANM) tailored for the high-temperature gas-cooled reactor (HTGR) analysis. The A-SANM has been crafted specifically for reactors with hexagonal geometries, such as the Vodo-Vodyanoi energetichesky reactor (VVER) and HTGR. A triangular node was constructed with a 12-term basis to delineate the flux by integrating both the polynomial and hyperbolic functions. The multigroup calculation kernel of this approach was embedded in the nodal diffusion code, RAST-V. To evaluate the computational efficiency of the A-SANM, we employed the MHTGR-350 benchmark. This benchmark, associated with a modular high-temperature gas-cooled reactor, was established by the OECD/NEA under the NGNP Project in 2021. In this study, we conducted the Phase I calculations to evaluate the performance of the neutronics code. Key parameters including the multiplication factor, rod worth, and axial and radial power distributions were meticulously assessed. When juxtaposed with the Monte Carlo code MCS, the A-SANM exhibited a deviation of –97 pcm. Differences in the axial and radial power were ± 4 and ± 3 %, respectively. Furthermore, the rod worth discrepancy was –6 pcm when set against the MCS. In summary, this study effectively elucidates the potential and precision of the multigroup A-SANM for the HTGR evaluations.
Cilj rada bio je opisati potencijal rasta prasadi s osvrtom na hranidbene zahtjeve prasadi prije i nakon faze odbića. Rast prasadi je opisan sigmoidnom krivuljom koju karakterizira brzi porast ...tijekom prve faze te blagi pad u drugoj fazi proizvodnog ciklusa. Kako bi se smanjila depresija rasta tijekom prvih dana nakon odbića važno je osigurati razdoblje prilagodbe tijekom kojeg će prasad prijeći s hranidbe majčinim mlijekom na hranidbu krutom hranom. Iako prasad posjeduje veliki kapacitet za brzi porast nakon razdoblja odbića on može biti ograničen čimbenicima kao što su dob pri odbiću, hranidba, mikrobiološki ili fiziološki čimbenici. Suplemenati poput esencijalnih ulja, aminokiselina, selena ili kratkolančanih masnih kiselina u obrocima pozitivno utječu na zdravstveni status prasadi, ali i na njihov potencijal za rast tijekom kasnijih faza proizvodnog ciklusa. Izbalansiranom hranidbom u pogledaju energije i hranjivih tvari osiguravaju se optimalni uvjeti za postizanje zadovoljavajućih prirasta uz zadržavanje dobrog zdravstvenog statusa prasadi što čini preduvjet uspješne svinjogojske proizvodnje.
The aim of this study was to describe the growth potential of weaned piglets with reference to the nutritional requirements of piglets before
and after the weaning. Piglets growth is described by sigmoid curve that is characterized with a rapid increase during the first stages and a
slight decrease in the second stage of the production cycle. In order to reduce growth depression during the first days after the weaning, it is important to provide an adjustment period during which the piglets will switch from feeding with sow’s milk to solid feeding. Although piglets possess a large capacity for rapid growth after the weaning, it may be limited by factors such as age at the weaning, feeding, microbiological or physiological factors. The addition of supplements such as essential oils, amino acids, selenium or short-chain fatty acids
in meals have a positive effect on the health status of piglets, but also on their growth potential during the later stages of the production
cycle. A balanced diet in terms of energy and nutrients ensures optimal
conditions for achieving satisfactory growth and maintaining good health status of piglets, which is a prerequisite for successful pig production.
In November 2018, the European Committee for Antimicrobial Susceptibility Testing (EUCAST) established rapid antimicrobial susceptibility testing (RAST), which could be performed directly on positive ...blood culture samples. Although concentrations of antimicrobial agents in several antimicrobial disks available in Japan are different from those recommended by the EUCAST, the feasibility of EUCAST RAST using antimicrobial disks available in Japan remains to be evaluated.
Blood culture bottles spiked with 127 clinical isolates (65 Escherichia coli and 62 Klebsiella pneumoniae) were tested by RAST for cefotaxime (CTX), ceftazidime (CAZ), meropenem, and ciprofloxacin using antimicrobial disks available in Japan, and compared with a reference AST method using automated AST instrument (VITEK®2).
The overall category agreement (CA) for RAST using antimicrobial disks available in Japan was 96.3%, 96.8%, and 95.6% after 4, 6, and 8 h of incubations, respectively.
However, the CAZ RAST for E. coli showed major error of 8.2% (8 h incubation) for the Sensi disk, 14.3% (6 h incubation), and 24.5% (8 h incubation) for the KB disk.
The CTX RAST for K. pneumoniae showed 25% (4 h incubation) and 31.3% (4 h incubation) of very major error for the Sensi and KB disks, respectively.
The EUCAST RAST results for E. coli and K. pneumoniae using antimicrobial disks available in Japan suggest their usefulness, although modified RAST breakpoints are required for several antimicrobial agents.
Adequate and timely antibiotic therapy is crucial for the treatment of sepsis. Innovative systems, like the Q-linea ASTar, have been developed to perform rapid antimicrobial susceptibility testing ...(AST) directly from positive blood cultures (BCs). We conducted a prospective study to evaluate ASTar under real-life conditions with a focus on time-to-result and impact on antimicrobial therapy. Over 2 months, all positive BCs that showed Gram-negative rods upon microscopy were tested with the ASTar and our standard procedure (VITEK 2 from short-term culture). Additionally, we included multidrug-resistant Gram-negative bacteria from our archive. Both methods were compared to broth microdilution. In total, 78 bacterial strains (51 prospective and 27 archived) were tested. ASTar covered 94% of the species encountered. The categorical and essential agreement was 95.6% and 90.7%, respectively. ASTar caused 2.4% minor, 2.0% major, and 2.4% very major errors. The categorical agreement was similar to standard procedure. The average time between BC sampling and the availability of the antibiogram for the attending physician was 28 h 49 min for ASTar and 44 h 18 min for standard procedure. ASTar correctly identified all patients who required an escalation of antimicrobial therapy and 75% of those who were eligible for de-escalation. In conclusion, ASTar provided reliable AST results and significantly shortened the time to obtain an antibiogram. However, the percentage of patients that will profit from ASTar in a low-resistance setting is limited, and it is currently unclear if a change of therapy 29 h after BC sampling will have a significant impact on the patient's prognosis.
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