The biochemical and microbiological characteristics of rumen fluid from cattle co-grazed with and without camels as compared to that from the foregut of camels

Suyub, Iswan (2014). The biochemical and microbiological characteristics of rumen fluid from cattle co-grazed with and without camels as compared to that from the foregut of camels PhD Thesis, School of Agriculture and Food Sciences, The University of Queensland. doi:10.14264/uql.2015.535

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Author Suyub, Iswan
Thesis Title The biochemical and microbiological characteristics of rumen fluid from cattle co-grazed with and without camels as compared to that from the foregut of camels
School, Centre or Institute School of Agriculture and Food Sciences
Institution The University of Queensland
DOI 10.14264/uql.2015.535
Publication date 2014-04-24
Thesis type PhD Thesis
Open Access Status Other
Supervisor Rafat Al Jassim
Mark Morrison
John Gaughan
Total pages 300
Language eng
Subjects 060101 Analytical Biochemistry
060102 Bioinformatics
060504 Microbial Ecology
Formatted abstract
Co-grazing is a common practice under many range conditions. The main advantage of co-grazing is to fully utilize the vegetation sources by taking advantage of the different preferences among animals towards plant species and parts. Hence, this study aimed to establish if co-grazing camels with cattle would lead to changes in the biochemical characteristics in the rumen contents of cattle, and result in different fermentation end products. Rumen contents were collected from two groups of animals at two different locations, the Runnymede Cattle Station at Richmond in northern Queensland, and the Meramist abattoir at Caboolture in Queensland. For the Richmond site, two groups of animals were sampled via stomach tube; cattle co-grazed with camels (n=6) and cattle grazed alone (n=6). For the Caboolture site, foregut contents from three groups of animals were sampled post mortem; camels co-grazed with cattle (n=6), cattle co-grazed with camels (n=6), and camels grazed alone (n=6). The ratios of camel to cattle for the Richmond and the Caboolture sites were 1:49 and 1:14 respectively. These ratios were considered adequate for microbial transfer to occur.

Foregut fluid samples from all animals were used to inoculate a pre-reduced medium containing Mitchell grass (Astrebla lappacea), Flinders grass (Iseilema spp.), or Lucerne hay (Medicago sativa). Measurements of gas production, volatile fatty acids, and dry matter digestibility were carried out following 48 or 96 h of in vitro incubation at 39 °C.

Inocula from cattle co-grazed with camels from Richmond resulted in greater (P< 0.05) dry matter digestibility for Mitchell grass than cattle grazed alone and produced greater (P< 0.05) amounts of n-butyrate. On the other hand, inocula of camels co-grazed with cattle from Caboolture had higher in vitro dry matter digestibility for Mitchell grass and shared the potential for higher dry matter digestibility with cattle co-grazed with camels for lucerne hay. Camels co-grazed with cattle also produced more (P<0.05) n-Butyric acid in the Mitchell grass treatment compared to groups of camels grazed alone and cattle co-grazed with camels. The results from the biochemical analysis suggested that co-grazing may change the ecosystem of the foregut in a number of beneficial ways.

A microbiological analysis was carried out to investigate the structure of the bacterial community in each group of animals with high throughput sequencing of 16s rRNA gene using 454 pyrosequencing technology. Using an open source software computational program provided by Quantitative Insights into Microbial Ecology (QIIME), not only was it possible to identify all microbial species within the foregut fluid samples but also it was possible for all data to be analysed and compared systematically.

Further analyses to identify the different operational taxonomic units (OTUs) with a similarity threshold of 97% allowed the assessment of observed species (OTUs); species richness (Chao1); and phylogenetic diversity (PD) whole tree metric for each foregut fluid sample. These analyses were sensitive enough to reveal both species abundance and species taxonomic or phylogenetic distances. Moreover, bacterial differences were also revealed at the phyla, family, and OTU levels.

A distinct pattern of the percentage of bacterial distribution evaluated at family taxonomical level was observed among the animal groups. In cattle co-grazed with camels from Richmond, Bacteroidales were the most abundant bacteria found (36%) while in cattle grazed alone Bacteroidales made up only 28%of the bacterial population. However, cattle grazed alone from Richmond had a higher percentage of Lachnospiraceae (19%) compared to cattle co-grazed with camels with only a 10% Lachnospiraceae population.

At the Caboolture site, camels grazed alone had the lowest Bacteroidales (20%) whilst the highest population was found in cattle co-grazed with camels (38%). In the group of camels co-grazed with cattle this group of bacteria accounted for 33%, which was lower than cattle co-grazed with camels. Prevotellaceae was highest in camels grazed alone (34%) and lower for camels co-grazed with cattle (26%). The lowest Prevotellaceae percentage was found in cattle co-grazed with camels at only 8%.

The principal coordinate analysis (PCoA) was also used to evaluate the samples. PCoA was performed by using the phylogenetic composition-base to plot each sample into one or more clusters so that a distance matrix measurement of variation could be constructed to reflect the corresponding dissimilarities of sample community membership or community structure. A clear clustering of all samples within its group was observed in PCoA analysis, which revealed a clear difference between groups of animals for both samples from the Richmond and the Caboolture sites.

These findings support the hypothesis that the GI tract is an interchange platform where adaptable microbial groups undergo a state of continuous replacement by functional bacterial species associated with changes in the environment. There is, however the possibility of indirect environmental contamination which might also be a factor influencing the occurrence of bacterial OTUs in multiple host species. Thus, additional research is needed to expand the investigations into all factors that are involved in the transformation that takes place in the foregut environment.
Keyword Co-grazing
Pyrosequencing
Camel
Rumen fluid
Microbe community structure
Foregut fermentation

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Created: Thu, 09 Apr 2015, 13:48:40 EST by Iswan Suyub on behalf of Scholarly Communication and Digitisation Service