Fecal microbiota of diarrheic calves: Before, during, and after recovering from disease

Aetiology and environmental factors of the Watery Mouth Disease associated with neonatal diarrhoea in lambs

Watery Mouth Disease is the main disease in neonatal lambs, causing great economic losses. Despite this, the cause of the condition remains poorly understood. Therefore, we have analysed the main bacteria found in sick animals, their intestinal and temporal distribution, as well as the main sources of contamination. Twelve different farms were sampled, from which 331 samples were taken in total. From these samples, 184 environments were analyzed using 16S rRNA amplicon sequencing, 164 isolates were identified by whole genome sequencing and 35 bacterial counts were performed. The dominant bacterial groups at the rectal level were Escherichia-Shigella (36 %) and Clostridium (29 %), with a homogeneous distribution along the digestive tract and a maximum abundance ranging between 12 and 24 hours of lamb life. Within Escherichia-Shigella: Escherichia coli and Escherichia fergusonii and within Clostridium: Clostridium perfringens, Clostridium cadaveris, Clostridium tertium and Clostridium paraputricum were identified as the main isolates present in sick animals. The high presence of Clostridium strains, especially potentially pathogenic species like C. perfringens in sick animals, point out Clostridium as a new important protagonist of watery mouth disease and the need of their inclusion in future studies. In particular, bedding was established as the main microbial contaminating factor, reaching the highest increase 48 hours after removal and cleaning of the lambing area (i.e. 8.03 ×108, 1.88 ×106, 3.88 ×106, 4.85 ×107 and 4.00 ×105 CFU/g for mesophilic aerobes, coliforms, E. coli, mesophilic anaerobes and sporulates, respectively). These results highlight the need to increase cleanliness in bedding to reduce the presence of these bacteria.