Succession of microbial communities in the gastrointestinal tract of calves during the monogastric phase

Submission note: A thesis submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy to the Department of Agriculture, School of Life Sciences, Faculty of Science, Technology and Engineering, La Trobe University, Bundoora.

The gastrointestinal tract (GIT) of an adult bovine ruminant contains millions of bacteria, archaea, protozoa, and fungi known as gut microbiota which are first acquired during birth. These microbial communities breakdown fibre, create energy, regulate immunity, promote cellular development, and generate methane. However, little is known about the presence of specific microorganisms and the change in their abundance in the GIT during the monogastric phase, particularly in response to diet. In the first three weeks of life, the monogastric phase, the GIT of a calf undergoes major changes that permit a dietary transition from milk to solid feed. The present study quantified the distribution and diversity of selected microorganisms in GIT compartments and faeces of calves during the monogastric phase from one hour after birth to 21 days of age. I report the earliest detection, one hour after birth, of fibrolytic bacteria, Geobacter spp., and methanogenic archaea in the GIT. Fibrolytic bacteria were detected in the rumen before the calves consumed solid fibre, suggesting that either fibrolytic bacteria used milk as a source of nutrients, or they used products from other species of microorganisms that consumed the milk. For the first time, Methanococcales, Methanomicrobiales, and Geobacter spp. were detected in calves. Geobacter spp. might use direct extracellular electron transfer to supply electrons to methanogenic archaea. Protozoa and general anaerobic fungi were not detected in the first four days of life. Differences in diet altered the concentrations of all detected microorganisms in the abomasum, caecum fluid, and caecum tissues. The concentrations of microorganisms in the faeces did not reflect the microbial concentrations in any other GIT compartment. The concentrations of the microbes was similar when sampled using either the post-mortem or stomach tube collection techniques, suggesting that either technique can be used when collecting ruminal fluid for microbiological examination. These pioneering microorganisms respond to change, hence they could be manipulated to enhance fibre digestion, reduce the weaning period, and decrease methanogenic archaea.