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Additional file 9: Table S3. Top five most frequently detected ROH in RIVER_DATA and SWAMP_DATA sets.

Additional file 12: Figure S7. Relationship between number of ROH and total length of the genome covered by ROH (using all ROH detected in ALL_DATA set).

Additional file 5: Table S2. Top ten most frequently detected ROH in the ALL_DATA set.

Additional file 3: Figure S2. Frequency distribution of ROH across chromosomes in river (black bars) and swamp (white bars) buffalo.

Additional file 2: Figure S1. Plot of linkage disequilibrium (r2) according to the distance between markers in river and swamp.

Additional file 8: Figure S6. Manhattan plot of smoothed FST values for chromosomes 1 to 24.

Additional file 7: Figure S5. Stacked bar graph of ROH distribution on BBU17 in river (a) and swamp (b) buffalo.

Additional file 4: Figure S3. Distribution of the average ROH length per chromosome in river (white bars) and swamp (black bars) buffalo populations.

Weaning is a stressful time for piglets, often leading to weight loss and is associated with increased morbidity and mortality. A leading cause for these post-weaning problems is enteric dysbiosis and methods to improve piglet health at this crucial developmental stage are needed. This study aimed to determine whether an enteric dysbiosis caused by weaning could be corrected via a faecal microbiota transplantation (FMT) from healthy piglets from a previous wean. Two or four focal piglets per litter were assigned to one of two treatments; FMT two days post weaning (n = 21; FMT) or a control which received saline two days post weaning (n = 21; CON). FMT consisted of homogenised donor faeces administered orally at 3 mL/kg. Weaning occurred at 18 days of age and weights and faecal samples were collected on days 18, 20, 24 and 35. 16S rRNA amplicon analysis was used to assess the faecal microbiota of piglets. FMT increased Shannon’s diversity post weaning (p < 0.001) and reduced the scratch score observed at 24 days of age (p < 0.001). The bacterial populations significantly differed in composition at each taxonomic level. In FMT pigs, significant increases in potentially pathogenic Escherichia coli were observed. However, increases in beneficial bacteria Lactobacillus mucosae and genera Fibrobacteres and Bacteroidetes were also observed in FMT treated animals. To our knowledge, this is the first study to observe a significant effect on piglet faecal microbiota following a single FMT administered post weaning. Therefore, FMT post weaning can potentially alleviate enteric dysbiosis.

Antimicrobial use in animals and the potential development of antimicrobial resistance is a global concern. So, non-antimicrobial techniques for animal disease control are needed. This study aimed to determine whether neonatal ceftiofur (CF) treatment affects piglet faecal microbiomes and whether faecal microbiome transplantation (FMT) can correct it. Two focal piglets per sow were assigned to treatments as follows: cffresh (n = 6) received CF (3 mg/kg intramuscular) at 7 d and fresh FMT at 13 d, cffrozen (n = 7) received CF at 7 d and frozen FMT at 13 d, CF (n = 8) received CF at 7 d and no FMT, and no CF (n = 5) received no CF or FMT. DNA was extracted from faecal samples collected on days 7, 13, and 18 for 16S rRNA amplicon analysis. All faecal blends used for the FMT consisted of pooled donor pig faeces at 1:2 ratio with saline, delivered orally at 3 mL/kg. Alpha and beta diversity metrics increased with age (p &lt, 0.05). However, no effect of antibiotic or FMT treatment was evident in 13 and 18 d old piglets (p &gt, 0.05). Although no effect of treatment was observed, information regarding microbial membership during lactation was gained.