During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and Protege as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.
Biology ; Dataset ; Gene Ontology ; Genome ; Genome, Microbial ; Geographic Information Systems ; Rumen* ; Semantics

The pathological changes of the gastric rumen produced by rocking stress in 38 young male albino rats fed on low protein diet for a short period and in 20 young male albino rats fed on low protein diet only as the control rats, were investigated macroscopically and histologically. The ulcerative lesions of the gastric rumen were observed in 17 out of 38 experimental rats accompanied with hyperplasia and cornification of the ruminal epithelial layer and more or less edematous changes of the tunica propria near the ulcer site. The authors, finding of the ruminal ulcer in albino rats produced by rocking stress associated with feeding on a low protein diet for a short period were compared with the results of others. The authors discussed other opinions concerning of the gastric ruminal ulcer of the albino rats produced in various ways.
Animal ; Male ; Protein Deficiency/complications* ; Rats ; Rumen* ; Stomach Ulcer/etiology* ; Stomach Ulcer/pathology ; Stress*

Here, we describe two cases of left displaced abomasum (LDA) in Holstein cattle at 6 and 9 months of twin gestation. Clinical examination revealed signs of proximal ileus with marked abdominal distension, but no ping sounds. An unusually high position of the gravid uterine horn on the left side was observed with ultrasound. Left exploratory laparotomy confirmed that the abomasum was displaced to the left and entrapped between the rumen and twin gravid uterine horn. A left surgical approach was necessary to correct the condition. Both animals recovered and gave birth to healthy twins. The present cases indicate that the subomental position of a heavy twin gravid uterine horn is a possible mechanical cause of LDA.
Abomasum ; Animals ; Cattle ; Displacement (Psychology) ; Horns ; Humans ; Ileus ; Laparotomy ; Parturition ; Pregnancy ; Pregnancy, Twin ; Rumen ; Twins ; Uterus

Recently, returning straw to the fields has been proved as a direct and effective method to tackle soil nutrient loss and agricultural pollution. Meanwhile, the slow decomposition of straw may harm the growth of the next crop. This study aimed to determine the effects of rumen microorganisms (RMs) on straw decomposition, bacterial microbial community structure, soil properties, and soil enzyme activity. The results showed that RMs significantly enhanced the degradation rate of straw in the soil, reaching 39.52%, which was 41.37% higher than that of the control on the 30th day after straw return. After 30 d, straw degradation showed a significant slower trend in both the control and the experimental groups. According to the soil physicochemical parameters, the application of rumen fluid expedited soil matter transformation and nutrient buildup, and increased the urease, sucrase, and cellulase activity by 10%‒20%. The qualitative analysis of straw showed that the hydroxyl functional group structure of cellulose in straw was greatly damaged after the application of rumen fluid. The analysis of soil microbial community structure revealed that the addition of rumen fluid led to the proliferation of Actinobacteria with strong cellulose degradation ability, which was the main reason for the accelerated straw decomposition. Our study highlights that returning rice straw to the fields with rumen fluid inoculation can be used as an effective measure to enhance the biological value of recycled rice straw, proposing a viable solution to the problem of sluggish straw decomposition.
Animals ; Rumen/metabolism* ; Agriculture/methods* ; Soil/chemistry* ; Microbiota ; Bacteria/metabolism* ; Oryza/metabolism* ; Soil Microbiology ; Cellulose

This study was carried out to evaluate the diagnosis of acute clinical mastitis (ACM) which was based on the vital signs and complete blood count (CBC) tests in dairy cows. Twenty eight dairy cows diagnosed with ACM, were selected for the study between Jan 2003 and July 2006 in the National Institute of Animal Science. Based on their vital signs (rectal temperature, depression, rumen contraction and, dehydration status), ACM was divided into three different classes; mild, moderate and severe forms. In addition, ACM cows were subjected to CBC tests for further diagnosis of ACM. Of the 27 dairy cows diagnosed with ACM, 3 cows were determined to have a mild form, while moderate and sever forms were each observed in twelve cows. Among of them, 4 cows died, 5 cows were culled and 18 cows were recovered. In the mild form, all haematological parameters were comparable with normal values. However, leukopenia, due to neutropenia and lymphocytopenia, appeared characteristically in the moderate and severe forms. Using the observation of vital signs in conjunction with CBC tests, the diagnosis of ACM is more accurate, and is helpful in making decisions of whether treatment or culling of dairy cows infected with ACM is most appropriate.
Animals ; Blood Cell Count ; Contracts ; Dehydration ; Depression ; Female ; Leukopenia ; Lymphopenia ; Mastitis ; Neutropenia ; Reference Values ; Rumen ; Vital Signs

PURPOSE: The absence of the oxalate-degrading bacteria, Oxalobacter formigenes, in the gastrointestinal tract correlates with the formation of calcium-oxalate urolithiasis. The aim of this study was to isolate Oxalobacter from human feces. MATERIALS AND METHODS: The OxB strain, isolated from sheep rumen, was incubated in selective growth media(medium B) in an anaerobic chamber, and its microbiological properties evaluated. Feces from volunteers, who were presumed to have O. formigenes from a polymerase chain reaction-based detection system, was incubated in medium B. The colonies isolated, primarily 7 days after incubation, were successively subcultured, and colony-PCR performed to isolate colonies from the successive subcultures. RESULTS: The colonies of OxB were Gram-negative, non-motile, non-spore forming, rod-shaped cells. The cells were often in pairs or chains. OxB DNA gave rise to an amplicon of the correct molecular size(416 bp) of O. formigenes. The morphology of the colonies from human feces, of which DNA was confirmed to have the same size amplicon of O. formigenes by PCR, was identical to the OxB, both grossly and by Gram stain. Although the morphology of the colonies isolated from the successive subcultures was no different from that of OxB, the PCR positivity of the isolated colonies decreased on successive subculturing, with no PCR-positive colonies from the fifth subculture. CONCLUSIONS: Our results suggest that the microbiological isolation and purification of Oxalobacter formigenes from human feces is a difficult procedure. Special culture conditions will be required to culture Oxalobacter species to reveal the link between O. formigenes and calcium oxalate urolithiasis in humans.
Bacteria ; Calcium Oxalate ; DNA ; Feces* ; Gastrointestinal Tract ; Humans* ; Kidney Calculi ; Oxalobacter formigenes* ; Polymerase Chain Reaction ; Rumen ; Sheep ; Urolithiasis ; Volunteers

In the present study, we report on the occurrence of paramphistomes, Fischoederius cobboldi and Paramphistomum epiclitum, in Lao PDR with the basis of molecular data. Parasite materials were collected from bovines bred in Ban Lahanam area, Savannakhet Province, Lao PDR at Lahanam public market. Morphological observations indicated 2 different species of paramphistomes. The mitochondrial gene cox1 of the specimens was successfully amplified by PCR and DNA sequencing was carried out for diagnosis of 11 specimens. Pairwise alignment of cox1 sequences were performed and confirmed F. cobboldi and P. epiclitum infecting bovines in Laos. Although there were many limiting points, as the small number of worm samples, and the restricted access of the animal host materials, we confirmed for the first time that 2 species of paramphistomes, F. cobboldi and P. epiclitum, are distributed in Lao PDR. More studies are needed to confirm the paramphistome species present in Savannakhet and its hosts to clear the natural history of these parasites of ruminants in the region and measure the impact of this parasite infection in the life and health of the local people.
Animals ; Cattle ; Diagnosis ; Genes, Mitochondrial ; Helminths ; Laos ; Natural History ; Paramphistomatidae* ; Parasites ; Polymerase Chain Reaction ; Rumen* ; Ruminants ; Sequence Analysis, DNA

The aflatoxin B1 degrading abilities of two different ruminants were compared in this study. One set of experiments evaluated the aflatoxin B1 degradation ability of different rumen fluid donors (steers vs. goats) as well as the rumen fluid filtration method (cheese cloth filtered vs. 0.45 microm Millipore) in a 2 x 2 factorial arrangement. Additional studies examined aflatoxin B1 degradation by collecting rumen fluid at different times (0, 3, 6, 9 and 12 h) after feeding. Cannulated Holstein steers (740 +/- 10 kg bw) and Korean native goats (26 +/- 3 kg bw) were fed a 60% timothy and 40% commercial diet with free access to water. Rumen fluid from Korean native goats demonstrated higher (p < 0.01) aflatoxin B1 degradability than Holstein steers. However, filtration method had no significant influence on degradability. In addition, aflatoxin degradation did not depend upon rumen fluid collection time after feeding, as no significant differences were observed. Finally, a comparison of two types of diet high in roughage found aflatoxin degradability in goats was higher with timothy hay opposed to rice straw, although individual variation existed. Thus, our findings showed the aflatoxin degradability is comparatively higher in goats compared to steers.
Aflatoxin B1/*chemistry/*metabolism ; Animals ; Body Fluids/*chemistry/metabolism ; Cattle/*physiology ; Goats/*physiology ; Korea ; Male ; Rumen/*metabolism

Calf losses have an economic impact on larger Korean native cattle (KNC) breeding farms due to replacement, productivity, and marketing. However, little research on KNC calf mortality or causes of calf death on large-scale breeding farms has been conducted. Based on medical records and autopsy findings from the Hanwoo experimental station of the National Institute of Animal Science, calf death records from 2002 to 2011 were used to identify the causes of mortality. Mortality rate of KNC calves was 5.7%. Large differences (1.8~12.6%) in year-specific mortalities were observed. Calf deaths were due to digestive diseases (68.7%), respiratory diseases (20.9%), accidents (6.0%), and other known diseases (2.2%). The main cause of calf death was enteritis followed by pneumonia, rumen indigestion, and intestinal obstruction. The greatest number of calf deaths occurred during the fall followed by summer. These results indicated that enteritis and pneumonia were the main reasons for calf death. However, autopsy findings demonstrated that other factors also caused calf death. This study suggested that seasonal breeding and routine vaccinations are the most important factors for preventing calf death, and improving calf health in high land areas with low temperature.
Animals ; Autopsy ; Breeding* ; Cattle ; Death Certificates ; Dyspepsia ; Efficiency ; Enteritis ; Intestinal Obstruction ; Marketing ; Medical Records ; Mortality* ; Pneumonia ; Rumen ; Seasons ; Vaccination

Using lipase segregation agar containing trioleoylglycerol, we obtained 18 lipase positive clones by screening from a metagenome library of dairy rumen microflora containing 15,360 clones. The average insert size of lipase positive clones was about 60 kb. Lipase enzyme activity analysis by p-NPP method indicated that Lipase6, Lipase7 and Lipase8 had higher lipolytic activities to substrates of p-nitrophenyl palmitate (C16), p-nitrophenyl alaurate (C12) and p-nitrophenyl palmitate (C16) respectively. The optimum pH of Lipase 6, Lipase 7 and Lipase 8 were 7.5. The halflife period of Lipase 8 with the value of 15 min in 70 degrees C decreased with the increase of temperature. In conclusion, the lipases screened in this study had different substrates specificity and good thermo stability, which laid a basis for large-scale industrial application.
Animals ; Bacteria ; genetics ; Cattle ; Cloning, Molecular ; Female ; Gene Library ; Lipase ; genetics ; metabolism ; Metagenome ; genetics ; Rumen ; microbiology ; Substrate Specificity ; Temperature