Neonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population-based studies of cattle have investigated how the microbiota is impacted during diarrhea. To characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves. Fifteen diarrheic calves between the ages of 1 and 30 days and 15 age-matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA). Significant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate. The fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.

Diarrhea is the leading cause of morbidity, mortality and antimicrobial drug use in calves during the first month of age. Alteration in the bacterial communities of the gastrointestinal tract occurs during diarrhea. Diarrheic calves often develop anion gap (AG) acidosis associated with increased concentrations of unmeasured anions including D- and L-lactate. However, studies investigating the association between gut microbiota alterations and the development of acid-base disorders in diarrheic calves are lacking. We investigated the fecal bacterial alterations of calves with diarrhea and its association with changes in blood pH, and AG. Blood and fecal samples from healthy and diarrheic veal calves were taken 7 days after arrival to the farm. The fecal microbiota of healthy and diarrheic calves was assessed by sequencing of 16S ribosomal RNA gene amplicons. Blood gas analysis was completed using an i-Stat analyzer. In healthy calves, higher richness, evenness, and diversity were observed compared to diarrheic calves.Phocaeicola, Bacteroides, Prevotella, Faecalibacterium, Butyricicoccus, Ruminococcaceae and Lachnospiraceae were enriched in healthy compared with diarrheic calves.Enterococcus, Ligilactobacillus, Lactobacilus, Gallibacterium Streptococcus, andEscherichia/Shigellawere enriched in diarrheic calves. In diarrheic calves, an increased abundance of lactate-producing bacteria includingLactobacillus, Streptococcus, Veillonella, LigilactobacillusandOlsenellawas detected. Diarrheic calves had a lower pH and bicarbonate concentration and a higher AG concentration than healthy calves. Together, these results indicate that calf diarrhea is associated with a shift from obligated to facultative anaerobes and expansion of lactate-producing bacteria which are related to acidemia, low bicarbonate and increase AG. Our results highlight the importance of the gastrointestinal microbiota on the clinicopathological changes observed in diarrheic calves.

Neonatal calf diarrhea is the leading cause of neonatal morbidity and mortality globally. The changes associated with the gastrointestinal microbiota in neonatal calves experiencing diarrhea and its etiology are not fully understood or completely defined in the literature. Several studies have demonstrated that the fecal microbiota of calves that experience diarrhea substantially deviates from that of healthy age-matched calves. However, one key question remains: whether the changes observed in the bacterial communities (also known as dysbiosis) are a predisposing factor for, or the consequence of, gastrointestinal inflammation caused by the pathogens associated with calf diarrhea. The first objective of this literature review is to present the current information regarding the changes in the fecal microbiota of diarrheic calves and the impact of the pathogens associated with diarrhea on fecal microbiota. Modulation of the gastrointestinal microbiota using pre- and probiotics, colostrum feeding, and fecal microbiota transplantation (FMT) has been used to treat and prevent gastrointestinal diseases in humans and dogs. Although information regarding the use of probiotics for the prevention of diarrhea is available in cattle, little information is available regarding the use of these strategies for treating calf diarrhea and the use of prebiotics or FMT to prevent diarrhea. The second objective of this literature review is to summarize the current knowledge regarding the impact of prebiotics, probiotics, synbiotics, colostrum feeding, and FMT for the treatment and prevention of calf diarrhea.

Feline fecal microbiota analyses can potentially be impacted by a variety of factors such as sample preparation, sequencing method and bioinformatics analyses. Another potential influence is changes in the microbiota from storage of samples prior to processing. This study examined the effect of ambient temperature exposure on the feline fecal microbiota composition. Fecal samples were collected from 12 healthy cats, within 15 min after defecation. Samples were aliquoted and the first aliquot was frozen at −80 °C within 1 hour of defecation. Remaining aliquots were maintained at ambient temperature (20 to 23 °C) and frozen at −80 °C at 6, 12, 24, 36, 48, 72 and 96 h after collection. DNA was extracted from all aliquots, and polymerase chain reaction (PCR). The PCR products were sequenced with next-generation sequencing (Illumina MiSeq). No significant differences were observed in alpha and beta biodiversity indexes, as well as relative abundance of different taxa over time (P > 0.05 for all tests between time points). Principal coordinate analyses demonstrated that samples cluster mainly by cat, with no significant differences between time points (AMOVA, P > 0.05; HOMOVA, P > 0.05). Linear discriminant analysis effect size method was performed and failed to detect any enriched taxa, between time points. Random forest algorithm analysis indicated homogeneity across time points. Although existing evidence from human fecal storage studies is contradictory, a recent study in companion animals agreed with the current study, demonstrating that maintenance of feline fecal samples at ambient temperature for up to 4 days has no effect on the bacterial membership and structure.