rRNA-based analysis to monitor succession of faecal bacterial communities in Holstein calves

Abstract

Aims: To quantitatively analyse the faecal bacterial communities of Holstein calves and track their succession up to 12 weeks of age. Methods and Results: Faecal samples obtained from four female Holstein calves were analysed by the RNA‐based, sequence‐specific rRNA cleavage method. Twelve scissor probes covering major rumen bacterial groups were used, detecting c. 60–90% of the total 16S rRNAs. At 1 week of age, 16S rRNAs from members of the Bacteroides‐Prevotella group (40·0% of the total 16S rRNAs), Faecalibacterium (21·7%), the Clostridium coccoides–Eubacterium rectale group (16·7%) and the Atopobium cluster (10·9%) were detected at high levels. Throughout the 12‐week period, rRNAs of the Bacteroides‐Prevotella and the Cl. coccoides‐Eu. rectale groups constituted the major fraction of microbiota (c. 50–70% of the total). The relative abundances of the Atopobium cluster, Faecalibacterium, and some probiotic bacteria (such as those of the genera Lactobacillus and Bifidobacterium) decreased as the animal aged. Instead, an uncultivated rumen bacterial group, as well as Ruminococcus flavefaciens and Fibrobacter emerged at the detectable levels (1–2%) in the faeces sampled at a postweaning age. In addition, certain bacterial groups that were not covered by the probe suite increased as the animals aged. Conclusions: Young calves undergo dynamic changes in their intestinal bacterial community during the first 12 weeks of life. As young ruminants undergo metabolic and physiological development in their digestive tracts in the transition from a monogastric to a ruminant animal at an early age, the intestinal bacterial community may reflect such development. Significance and Impact of the Study: The succession of the bacterial communities in the faeces of calves was quantitatively monitored in the present study for the first time. The approach used here was demonstrated to be a useful means for determining the populations of predominant faecal bacterial groups in a variety of calf experiments in response to diet, stress and disease.

Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

“…The high proportion of assigned genus information observed in the large-intestinal communities may be due to their resemblance to the fecal bacterial community, which has been studied more extensively than the small intestine community. Uyeno and colleagues reported that the fecal microbiomes of 3-week-old dairy calves consist of 39.2% BacteroidesPrevotella group, 17.7% Clostridium coccoides-Eubacterium rectale group, and 11% Faecalibacterium (8). Colon samples from the 3-week-old calves used in the present study revealed similar levels for the Bacteroides-Prevotella group (32.5%) and Faecalibacterium (12.1%).…”

“…The fecal bacterial composition of dairy calves undergoes dynamic changes during the first 12 weeks of life (8). These changes include the appearance of new species such as Ruminococcus flavefaciens and Fibrobacter species and the disappearance of Bifidobacterium, Enterobacteriaceae, Streptococcus, and Lactobacillus species (8), suggesting that both diet and gut development may drive changes in the bacterial composition during early life.…”

“…These changes include the appearance of new species such as Ruminococcus flavefaciens and Fibrobacter species and the disappearance of Bifidobacterium, Enterobacteriaceae, Streptococcus, and Lactobacillus species (8), suggesting that both diet and gut development may drive changes in the bacterial composition during early life. A study comparing mucosa-and digesta-associated bacterial phylotypes in preweaned calves revealed a much greater richness in mucosa-associated bacterial phylotypes throughout the GIT than in those in the regional digesta (9).…”

Faecal culturable microbiota, growth and clinical parameters of calves supplemented with lactic acid bacteria and lactose prior and during experimental infection with Salmonella Dublin DSPV 595T

“…Cultural methods used in this work are useful for the quantification of specific populations. To determine a change in any of the predominant populations in the complex intestinal microbiota is suggested to use rRNA-based analysis (Mayer et al 2012, Uyeno et al 2010.…”

Effects of cellooligosaccharide or a combination of cellooligosaccharide and live Clostridium butyricum culture on performance and intestinal ecology in Holstein calves fed milk or milk replacer

“…The prokaryotic cells in 1 ml of 152 the suspensions were disrupted by glass bead beating (Uyeno et al, 2010a), and the total 153 RNAs were extracted with 1 ml of phenol equilibrated with a buffer consisting of 10 154 mmol/l EDTA, 50 mmol/l sodium acetate (pH 5.1). Aliquots of 0.5 ml of the aqueous 155 phase were obtained by centrifugation for 5 min at 12000  g at 4°C, followed by 156 purification using an RNeasy mini kit (Qiagen, calculation to determine the 16S rRNA population of the target group in total 16S 166 rRNAs were performed as described previously (Uyeno et al, 2007).…”