The Colonization And Temporal Dynamics Of The Gut Microbiota In Chengdu Brown Goat Kids From Birth-up To 56-day-old

The colonization of the microbiota is crucial for the gut development in young animals.The beneficial gut microorganisms can be involved in the digestion and absorption of various nutrients,and thereby contribute to the normal physiological function of the gut.In this study,we collected fecal samples of Chengdu Brown goat kids(n = 11)in seven time points ranging from birth-up to 56-day-old(days 0,7,14,21,28,42,and 56),and the microorganism samples in four body sties of the respective mothers(n = 9).By using 16 S r RNA gene sequencing,we investigated the sources,colonization,and temporal dynamics of the gut microbiota in goat kids.The main results were as follow:In this study,the microbiota in four body sites(i.e.,the breast milk,feces,vagina,and oral cavity)of mothers(the mothers of goat kids)were regarded as potential sources.Based on the analysis with Source Tracker,the results showed that the average contribution of microorganisms in the vagina and breast milk were 40.81% and 17.12%,respectively,which could be considered as the main sources.With the increase of the age of goat kids,the contribution of microbiota in the breast milk and vagina of mothers to the gut microbiota of goat kids generally decreased(breast milk: 21% ～ 9.10%,vagina: 58.15% ～17.78%),whereas the contribution of fecal microbiota of motherss increased rapidly(1.05%～ 21.02%)from day 28 to day 56.Furthermore,the proportion of unknown microorganisms rose gradually with age(12.58% ～ 51.18%).The results of alpha analysis showed that the evenness(Shannon index: 3.52～6.94)and richness(Chao1 index: 157～591)of gut microbiota in goat kids increased significantly with age.According to the PCo A analysis(variance explained = 32.28% and 16.60% for the first and second coordinates,respectively)using an unweighted Uni Frac metric,all the microbial samples(n = 71)can be divided into two large groups: days 0,7,14,and 21;days 28,42,and 56.Furthermore,based on the above analyses of diversity and similarity as well as previous reports,the gut microbiota in goat kids can be classified into three temporal stages: newborns(day 0),the non-rumination stage(days 7 ～ 21),and the transition stage(days 28 ～ 56).In total,21 bacterial phyla were found in the gut(n = 71)of goat kids from birth-up to56-day-old.The predominant phyla mainly included Firmicutes(49.90%),Bacteroidetes(27.73%),and Proteobacteria(19.76%),whereas the relative abundance of these three phyla fluctuated greatly with age.We discovered a total of 624 bacterial genera in the gut of goat kids at all seven time points.In addition to Bacteroides showing the highest overall average proportion(16.90%),other dominant genera belonging to Bacteroidetes consisted of Parabacteroides(4.40%)and Alistipes(3.46%).In the Firmicutes,the dominant genera mainly included Lactobacillus(4.95%),Ruminococcaceae UCG-005(4.01%),Butyricicoccus(3.93%),and Ruminococcaceae UCG-014(2.53%).Furthermore,Escherichia-Shigella and Desulfovibrio,two members of Proteobacteria,showed a high proportion of 13.27% and 2.05%,respectively.We identified a total of 49 unique bacterial biomarkers across the gut of goat kids at three temporal stages(newborn,non-rumination,and transition stages)using the LEf Se analysis(LDA score > 3 and P < 0.05).Nine bacterial taxa,including Staphylococcaceae,Enterobacteriaceae and its two members(i.e.,Escherichia-Shigella and Citrobacter),were detected as biomarkers in gut of newborn goat kids(day 0).Eight and seven out of 15 biomarkers identified at the non-rumination stage(days 7 to 21)belongs to Firmicutes(e.g.,Lactobacillaceae,Lactobacillus,and Butyricicoccus)and Bacteroidetes(e.g.,Bacteroidetes,Bacteroidaceae,Bacteroides,Alistipes),respectively.In addition to,Firmicutes and its 13 members(e.g.,Ruminococcaceae,Lachnospiraceae,Ruminococcaceae UCG＿014,Ruminococcaceae UCG＿005,and Faecalibacterium),the biomarkers at the transition stage(days 28 to 56)mainly included Prevotellaceae and Muribaculaceae belonging to Bacteroidetes,and Succinivibrionaceae and Succinivibrio belonging to Proteobacteria.Among the total of 49 bacterial biomarkers identified above,33 biomarkers showed significant Spearman correlations(P < 0.05)with individual VFAs or total VFA in gut of goat kids(n = 71).The 11 significant acetate-associated biomarkers mainly included Bacteroidetes,Bacteroidaceae,Lactobacillaceae,Bacteroides,and Lactobacillus(ρ <-0.17).The propionate was positively associated with seven biomarkers,including Bacteroidetes and its members(e.g.,Rikenellaceae,Muribaculaceae,and Alistipes)(ρ >0.17),whereas there were significant negative correlations(ρ <-0.16)between propionate and nine biomarkers(e.g.,Firmicutes,Citrobacter,and Marinospirillum).Significant positive correlations were present between butyrate and the Firmicutes and its members(e.g.,Clostridia,Lactobacillaceae,and Lactobacillus)(ρ > 0.12),as opposed to its negative relations to Prevotellaceae and Rikenellaceae(ρ <-0.08).Furthermore,17 biomarkers significantly related to isobutyrate(positive correlation: 12 biomarkers;negative correlation: five biomarkers).The dominant bacterial phylum in the rumen of 56-day-old goat kids and goats mainly included Bacteroidetes(47.90% and 52.44%),Firmicutes(47.03% and 42.14%)and Proteobacteria(2.51% and 3.15%).At the genus level,Prevotella showed the highest relative abundances(20.00% and 24.21%)in the rumen of 56-day-old goat kids and goats,followed by Rikenellaceae RC9 gut group(9.73% and 12.19%),Christensenellaceae R-7group(6.49% and 4.83%),and Ruminococcaceae NK4A214 group(5.01% and 4.06%).There were no significant differences(P < 0.05)in the concentration of total VFA and proportions of individual VFAs in the rumen between 56-day-old goat kids and mothers,except for butyrate and valerate.In summary,the results showed that the microbiota in the vagina and breast milk of goats were considered the main sources of the gut microbiota in goat kids.The distinct stage-associated gut microbiota in goat kids may be determined by the differences in gut physiology and/or at diet different growth stages.Although there were some differences in rumen microbial community structure between 56-day-old goat kids to mothers,and the composition of dominant bacteria was similar.