Background 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. Results 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. Conclusions 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. Electronic supplementary material The online version of this article (10.1186/s40168-019-0721-7) contains supplementary material, which is available to authorized users.

In 1989, Fuller defined a probiotic as 'a live microbial feed supplement which beneficially affects the host animal by improving its intestinal microbial balance', thereby emphasising the importance of live cells. In the strictest sense of this definition, it may be premature to describe fungal additives given to ruminants as probiotics, as although they are active in the rumen, post-ruminal effects cannot be ruled out, and the requirement for live cells has not been totally established.The rumen environment can be altered by using chemicals, or with the use of antibiotic/microbial fermentation products; however, the fact that fungal cultures containing either live or dead cells may play a significant role in controlling rumen fermentation is new. Two fungal cultures have received considerable attention.Saccharomyces cerroisiae ( 5 x 10' live organisms g -' plus growth medium) (yeast culture) (SC) and Aspergillus oryzur (a fungal additive) (OA) have been shown to increase productivity of ruminants (c. 5-7% increase in fat-corrected milk yield in lactating dairy cows) when added in small quantities to the diet. At present, the work carried out with SC has involved the use of yeast strain 1026; results in the literature indicate that the strain of organism is important. The increase in production results from an increase in feed intake, and at present there has been no need to postulate a more fundamental metabolic response. Increased feed intake has been related to increases in the rate of degradation of fibrous materials in the rumen and to effects on rumen fermentation patterns.Evidence suggests that to be effective in the rumen the fungal microorganisms do not need t o reproduce; however, this does not rule out the fact that the cells need t o be metabolically active. The cells retain viability in the rumen, and increased numbers of viable yeast cells are found at the proximal duodenum and terminal ileum. Measurements of the effects of the addition of fungal cultures to the diet on the degradability of hay or straw incubated in nylon bags has shown that the initial rate of degradation is increased by approximately 20% but there is no effect on the potential degradability. These results have been confirmed by measurement of cellulose digestion in pure or co-culture of SC with Bacteroides succinoyenes. This indicates that the activity of fungal cultures is directed more

Two hundred sixteen crossbred barrows and gilts (84.3 kg BW) were used to test the effects of dietary energy density and lysine:energy ratio (Lys:ME) on the performance, carcass characteristics, and pork quality of finishing pigs fed 10 ppm ractopamine. Pigs were blocked by BW and gender, allotted to 36 pens (six pigs per pen), and pens were assigned randomly within blocks to dietary treatments (as-fed basis) arranged in a 2 x 3 factorial design, with two levels of energy (3.30 or 3.48 Mcal/kg) and three Lys:ME (1.7, 2.4, or 3.1 g lysine/Mcal) levels. Pigs were fed experimental diets for 28 d, and weights and feed disappearance were recorded weekly to calculate ADG, ADFI, and G:F. Upon completion of the feeding trial, pigs were slaughtered and carcass data were collected before fabrication. During carcass fabrication, hams were analyzed for lean composition using a ham electrical conductivity (TOBEC) unit, and loins were collected, vacuum-packaged, and boxed for pork quality data collection. Energy density had no (P> 0.22) effect on ADG or ADFI across the entire 28-d feeding trial; however, pigs fed 3.48 Mcal of ME were more (P < 0.02) efficient than pigs fed 3.30 Mcal of ME. In addition, ADG and G:F increased linearly (P < 0.01) as Lys:ME increased from 1.7 to 3.1 g/Mcal. Carcasses of pigs fed 3.48 Mcal of ME were fatter at the last lumbar vertebrae (P < 0.08) and 10th rib (P < 0.04), resulting in a lower (P < 0.03) predicted fat-free lean yield (FFLY). Conversely, 10th-rib fat thickness decreased linearly (P = 0.02), and LM depth (P < 0.01) and area (P < 0.01) increased linearly, with increasing Lys:ME. Moreover, FFLY (P < 0.01) and actual ham lean yield (P < 0.01) increased as Lys:ME increased in the diet. Dietary energy density had no (P > 0.19) effect on pork quality, and Lys:ME did not (P > 0.20) affect muscle pH, drip loss, color, and firmness scores. Marbling scores, as well as LM lipid content, decreased linearly (P < 0.01) as Lys:ME increased from 1.7 to 3.1 g/Mcal. There was a linear (P < 0.01) increase in shear force of cooked LM chops as Lys:ME increased in the finishing diet. Results indicate that 3.30 Mcal of ME/kg (as-fed basis) is sufficient for optimal performance and carcass leanness in pigs fed ractopamine. The Lys:ME for optimal performance and carcass composition seems higher than that currently used in the swine industry; however, feeding very high Lys:ME (> 3.0 g/Mcal, as-fed basis) to ractopamine-fed pigs may result in decreased marbling and cooked pork tenderness.

A direct-fed microbial (DFM) based on a combination of Bacillus organisms specifically selected to increase the manure decomposition process was evaluated to determine its efficacy for improving growth performance and manure dissolution time. Three experiments involving 336 crossbred barrows and gilts were conducted to determine the effect of the Bacillus-based direct-fed microbial on growth performance and pen cleaning time. In each experiment, 2 dietary treatments (0 and 0.05% DFM) were fed during the growing-finishing period throughout the experiment, such that the DFM provided 1.47 x 10(8) cfu of Bacillus organisms per gram of supplement. Data from the 3 experiments were combined for analysis, such that there were 28 pens representing each of the 2 treatments. Pigs were weighed and feed intake was determined at the initiation and termination of each phase (starter, grower, and finisher). At the end of Exp. 1 and 3, pen cleaning time was determined by measuring the time required for each pen to be scraped and washed with a high-pressure sprayer. Additionally, 2 solid manure mat samples weighing approximately 4 g each were collected from solid manure buildup in each pen (16 pens/treatment), and the time required to completely disperse each manure mat sample was determined. Gain:feed improved (P < 0.05) in pigs fed Bacillus compared with the control diet during the finisher phase and throughout the combined growing-finishing period. The time required to dissolve the manure mat was reduced (P < 0.01) in samples collected from pens containing pigs fed Bacillus compared with samples from control pens. An additional evaluation was conducted in a commercial swine production facility using statistical process control analysis. Statistical process control analysis determined that supplementation with Bacillus increased the expected mean for ADG and decreased the expected mean for death loss percentage. Supplementation with a DFM composed of specifically selected Bacillus organisms improved G:F and decreased the time required to disperse a swine manure mat sample in a controlled study conducted at swine research facilities. Furthermore, when evaluated in a commercial swine production facility, the Bacillus-based DFM improved ADG and reduced mortality of pigs during the growing-finishing period.

Two experiments were conducted to determine the efficacy of mannan oligosaccharides (MOS) fed at two levels of Cu on growth and feed efficiency of weanling and growing-finishing pigs, as well as the effect on the immunocompetence of weanling pigs. In Exp. 1, 216 barrows (6 kg of BW and 18 d of age) were penned in groups of six (9 pens/treatment). Dietary treatments were arranged as a 2 x 2 factorial consisting of two levels of Cu (basal level or 175 ppm supplemental Cu) with and without MOS (0.2%). Diets were fed from d 0 to 38 after weaning. Blood samples were obtained to determine lymphocyte proliferation in vitro. From d 0 to 10, ADG, ADFI, and gain:feed (G:F) increased when MOS was added to diets containing the basal level of Cu, but decreased when MOS was added to diets containing 175 ppm supplemental Cu (interaction, P < 0.01, P < 0.10, and P < 0.05, respectively). Pigs fed diets containing 175 ppm Cu from d 10 to 24 and d 24 to 38 had greater (P < 0.05) ADG and ADFI than those fed the basal level of Cu regardless of MOS addition. Pigs fed diets containing MOS from d 24 to 38 had greater ADG (P < 0.05) and G:F (P < 0.10) than those fed diets devoid of MOS. Lymphocyte proliferation was not altered by dietary treatment. In Exp. 2, 144 pigs were divided into six pigs/pen (six pens/treatment). Dietary treatments were fed throughout the starter (20 to 32 kg BW), grower (32 to 68 kg BW), and finisher (68 to 106 kg BW) phases. Diets consisted of two levels of Cu (basal level or basal diet + 175 ppm in starter and grower diets and 125 ppm in finisher diets) with and without MOS (0.2% in starter, 0.1% in grower, and 0.05% in finisher). Pigs fed supplemental Cu had greater (P < 0.05) ADG and G:F during the starter and grower phases compared to pigs fed the basal level of Cu. During the finisher phase, ADG increased when pigs were fed MOS in diets containing the basal level of Cu, but decreased when MOS was added to diets supplemented with 125 ppm Cu (interaction, P < 0.05). Results from this study indicate the response of weanling pigs fed MOS in phase 1 varied with level of dietary Cu. However, in phase 2 and phase 3, diets containing either MOS or 175 ppm Cu resulted in improved performance. Pharmacological Cu addition improved gain and efficiency during the starter and grower phases in growing-finishing pigs, while ADG response to the addition of MOS during the finisher phase seems to be dependent upon the level of Cu supplementation.