Despite recent advances in the understanding of the swine gut microbiome at different growth stages, a comprehensive longitudinal study of the lifetime (birth to market) dynamics of the swine gut microbiome is lacking. To fill in this gap of knowledge, we repeatedly collected a total of 273 rectal swabs from 18 pigs during lactation (day (d) 0, 11, 20), nursery (d 27, 33, 41, 50, 61), growing (d 76, 90, 104, 116), and finishing (d 130, 146, 159, 174) stages. DNA was extracted and subjected to sequencing with an Illumina Miseq sequencer targeting the V4 region of the 16S rRNA gene. Sequences were analyzed with the Deblur algorithm in the QIIME2 package. A total of 19 phyla were detected in the lifetime pig gut microbiome with Firmicutes and Bacteroidetes being the most abundant. Alpha diversity including community richness (e.g., number of observed features) and diversity (e.g., Shannon index) showed an overall increasing trend. Distinct shifts in microbiome structure along different growth stages were observed. LEfSe analysis revealed 91 bacterial features that are stage-specific. To validate these discoveries, we performed fecal microbiota transplantation (FMT) by inoculating weanling pigs with mature fecal microbiota from a growing stage pig. Similar stage-specific patterns in microbiome diversity and structures were also observed in both the FMT pigs and their littermates. Although FMT remarkably increased growth performance, it did not change the overall swine gut microbiome. Only a few taxa including those associated with Streptococcus and Clostridiaceae were enriched in the FMT pigs. These data, together with several other lines of evidence, indicate potential roles these taxa play in promoting animal growth performance. Diet, especially crude fiber from corn, was a major factor shaping the swine gut microbiome. The priority effect, i.e., the order and timing of species arrival, was more evident in the solid feed stages. The distinct stage-associated swine gut microbiome may be determined by the differences in diet and/or gut physiology at different growth stages. Our study provides insight into mechanisms governing gut microbiome succession and also underscores the importance of optimizing stage-specific probiotics aimed at improving animal health and production.

Background: The greatest impact on profitability of a commercial beef operation is reproduction. However, in beef heifers, little is known about the vaginal and fecal microbiota with respect to their relationship with fertility. To this end, we followed heifers through gestation to examine the dynamics of vaginal and fecal microbial composition throughout pregnancy.Results: Heifers were exposed to an estrus synchronization protocol, observed over a 12-day period, artificially inseminated 12 h to 18 h after observed estrus, and subsequently exposed to bulls for a 50-day breeding season. Vaginal samples were taken at pre-breeding (n = 72), during the first (n = 72), and second trimester (n = 72) for all individuals, and third trimester for individuals with confirmed pregnancies (n = 56). Fecal samples were taken at pre-breeding (n = 32) and during the first trimester (n = 32), including bred and open individuals. Next generation sequencing of the V4 region of the16S rRNA gene via the Illumina MiSeq platform was applied to all samples. Shannon indices and the number of observed bacterial features were the same in fecal samples. However, significant differences in vaginal microbiome diversity between gestation stages were observed. No differences in beta-diversity were detected in vaginal or fecal samples regarding pregnancy status, but such differences were seen with fecal microbiome over time. Random Forest was developed to identify predictors of pregnancy status in vaginal (e.g.,Histophilus, Clostridiaceae,Campylobacter) and fecal (e.g., Bacteroidales,Dorea) samples.Conclusions: Our study shows that bovine vaginal and fecal microbiome could be used as biomarkers of bovine reproduction. Further experiments are needed to validate these biomarkers and to examine their roles in a female’s ability to establish pregnancy.

Weaning is one of the most stressful events in the life of a pig. Unsuccessful weaning often leads to intestinal and immune system dysfunctions, resulting in poor growth performance as well as increased morbidity and mortality. The gut microbiota community is a complex ecosystem and is considered an “organ,” producing various metabolites with many beneficial functions. In this review, we briefly introduce weaning-associated gut microbiota dysbiosis. Then, we explain the importance of maintaining a balanced gut microbiota. Finally, we discuss dietary supplements and their abilities to restore intestinal balance and improve the growth performance of weaning pigs.

Feed additives have been suggested to improve animal growth performance through modulating the gut microbiota. The hypothesis of this study was that the combination of two organic acids would exert synergistic effects on the growth performance and gut microbiota of weaning pigs. To test this hypothesis, we followed 398 weaning pigs from two university experiment stations (University of Illinois at Urbana-Champaign (UIUC) and University of Arkansas (UA)) to determine the effects of increasing levels (0%, 0.035%, 0.070%, and 0.105%) of sodium butyrate combined with 0.5% benzoic acid on the growth performance of nursery pigs. At the UA, an additional negative control diet was included and the gut microbiota analysis was carried out. At both universities, increasing levels of sodium butyrate in a diet containing 0.5% benzoic acid improved growth performance, which reached a plateau in the pigs fed 0.035% (SBA0.035) or 0.070% (SBA0.070) butyrate. Gut microbiota analysis revealed that pigs fed the SBA0.035 diet had more diverse microbiota and contained more potentially beneficial bacteria such as Oscillospira, Blautia, and Turicibacter and reduced levels of Veillonella and Sarcina. Results of the present study indicated that the inclusion of sodium butyrate at moderate levels in a diet containing 0.5% benzoic acid improved growth performance of weaning pigs and established potential health benefits on gut microbiota.

The fermented feed has been used extensively as a growth promoter in agricultural animal production. However, the effects of fermented feed on swine gut microbiota are still largely unknown. The work presented here aimed to investigate the growth performance and gut microbiota of nursery pigs receiving the LPF diet (10% Lactobacillus plantarum and Pediococcus acidilactici co-fermented feed + basal diet) compared with pigs receiving the NC diet (basal diet). The data showed LPF diet numerically improved average daily gain and significantly increased fecal acetate, butyrate, and total short-chain fatty acid (SCFA) concentrations. Furthermore, gut microbiota structure and membership significantly changed in response to the addition of fermented feed in the diet. Gut microbiota results indicated that LPF treatment significantly enriched SCFA-producing bacteria such as Megasphaera, Roseburia, Faecalibacterium, Blautia, Selenomonas, Dialister, Acidaminococcus, Ruminococcus, and Bifidobacterium. Some of these bacteria also had anti-inflammatory and other beneficial functions. Overall, these findings suggested that Lactobacillus plantarum and Pediococcus acidilactici co-fermented feed benefited growth performance and established potential health impacts on the gut microbiota of nursery pigs.