Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets

BACKGROUND

Age-associated changes in the gastrointestinal microbiome of young pigs have been robustly described; however, the temporal dynamics of the fecal microbiome of the female pig from early life to first parity are not well understood. Our objective was to describe microbiome and antimicrobial resistance dynamics of the fecal microbiome of breeding sows from early life through estrus, parturition and weaning of the first litter of piglets (i.e., from 3 to 53 weeks of age).

RESULTS

Our analysis revealed that fecal bacterial populations in developing gilts undergo changes consistent with major maturation milestones. As the pigs progressed towards first estrus, the fecal bacteriome shifted from Rikenellaceae RC9 gut group- and UCG-002-dominated enterotypes to Treponema- and Clostridium sensu stricto 1-dominated enterotypes. After first estrus, the fecal bacteriome stabilized, with minimal changes in enterotype transition and associated microbial diversity from estrus to parturition and subsequent weaning of first litter piglets. Unlike bacterial communities, fecal fungal communities exhibited low diversity with high inter- and intra-pig variability and an increased relative abundance of certain taxa at parturition, including Candida spp. Counts of resistant fecal bacteria also fluctuated over time, and were highest in early life and subsequently abated as the pigs progressed to adulthood.

CONCLUSIONS

This study provides insights into how the fecal microbial community and antimicrobial resistance in female pigs change from three weeks of age throughout their first breeding lifetime. The fecal bacteriome enterotypes and diversity are found to be age-driven and established by the time of first estrus, with minimal changes observed during subsequent physiological stages, such as parturition and lactation, when compared to the earlier age-related shifts. The use of pigs as a model for humans is well-established, however, further studies are needed to understand how our results compare to the human microbiome dynamics. Our findings suggest that the fecal microbiome exhibited consistent changes across individual pigs and became more diverse with age, which is a beneficial characteristic for an animal model system.

Age influences the temporal dynamics of microbiome and antimicrobial resistance genes among fecal bacteria in a cohort of production pigs

BACKGROUND

The pig gastrointestinal tract hosts a diverse microbiome, which can serve to select and maintain a reservoir of antimicrobial resistance genes (ARG). Studies suggest that the types and quantities of antimicrobial resistance (AMR) in fecal bacteria change as the animal host ages, yet the temporal dynamics of AMR within communities of bacteria in pigs during a full production cycle remains largely unstudied.

RESULTS

A longitudinal study was performed to evaluate the dynamics of fecal microbiome and AMR in a cohort of pigs during a production cycle; from birth to market age. Our data showed that piglet fecal microbial communities assemble rapidly after birth and become more diverse with age. Individual piglet fecal microbiomes progressed along similar trajectories with age-specific community types/enterotypes and showed a clear shift from E. coli/Shigella-, Fusobacteria-, Bacteroides-dominant enterotypes to Prevotella-, Megaspheara-, and Lactobacillus-dominated enterotypes with aging. Even when the fecal microbiome was the least diverse, the richness of ARGs, quantities of AMR gene copies, and counts of AMR fecal bacteria were highest in piglets at 2 days of age; subsequently, these declined over time, likely due to age-related competitive changes in the underlying microbiome. ARGs conferring resistance to metals and multi-compound/biocides were detected predominately at the earliest sampled ages.

CONCLUSIONS

The fecal microbiome and resistome-along with evaluated descriptors of phenotypic antimicrobial susceptibility of fecal bacteria-among a cohort of pigs, demonstrated opposing trajectories in diversity primarily driven by the aging of pigs.

Effects of mat feeding on the growth performance, removal, and mortality of pigs after weaning

Four experiments were conducted to determine the effect of mat feeding strategy on the growth performance, removal, and mortality of pigs after weaning. In exp. 1, 1,392 weanling pigs (initially 7.0 kg; approximately 24 d of age) were randomly allotted to 1 of 2 mat feeding treatments (mat feed vs. no mat feed). Overall, mat fed pigs had a tendency for improved ADG (P = 0.065) and G:F (P = 0.060) compared to pigs not offered mat feed. Mat fed pigs had fewer removals (P = 0.013) compared to pigs not offered mat feed. In exp. 2, 2,912 weanling pigs (initially 5.5 kg; approximately 21 d of age) were randomly allotted to 1 of 2 mat feeding treatments (mat feed vs. no mat feed). Overall, no differences in growth performance were observed. However, mat fed pigs had decreased (P < 0.026) final body weights compared to pigs not offered mat feed. This may be related to removal rates as mat fed pigs had fewer removals (P = 0.026). In exp. 3, 3,264 weanling pigs (initially 5.5 kg; approximately 21 d of age) were randomly allotted to 1 of 4 treatments in a 2 × 2 factorial with main effects of diet form (pellet or crumble) and mat feeding (mat feed vs. no mat feed). No interactions between diet form and mat feeding were observed. No differences were observed in overall growth performance for the main effect of mat feeding. Pigs offered pelleted feed had decreased overall ADFI (feed disappearance from the feeder and feed placed on the mat; P = 0.013) and improved G:F (P < 0.001) compared to pigs offered crumble feed. No differences were observed in removals or mortalities for the main effect of mat feeding or diet form. In exp. 4, 3,227 weanling pigs (initially 5.1 kg; approximately 21 d of age) were randomly allotted to 1 of 3 treatments consisting of mat feeding small (3.2 mm) pellets, mat feeding large (12.7 mm) pellets, or no mat feeding. Overall, no differences were observed in ADG or G:F. Mat fed pigs had increased ADFI (P < 0.001) compared to pigs not offered mat feed. Given the shorter duration of this experiment, the extra feed provided with mat feeding had a greater impact on overall feed usage than exp. 1, 2, and 3. No differences were observed in removals or mortalities. When combining the removal and mortality data for the four experiments, mat fed pigs had fewer removals (P = 0.002) compared to pigs not offered mat feed. In summary, mat feeding may encourage earlier feeding behavior, therefore reducing the removal rate of pigs post-weaning.

Impact of added copper, alone or in combination with chlortetracycline, on growth performance and antimicrobial resistance of fecal enterococci of weaned piglets

Studies suggest a link between added copper (Cu) and co-selection of antimicrobial resistance (AMR) in Enterococcus spp., but data are inconsistent. This study aimed to assess the impact of added Cu, alone or with a feed-grade antimicrobial, on growth performance, transferable Cu resistance gene (tcrB) prevalence, abundance of tcrB in fecal community DNA, and AMR in fecal enterococci in weaned piglets. A total of 320 barrows (DNA 200 × 400, DNA Genetics) weaned at approximately 21 d of age with 7.4 kg (7.4 ± 0.06 kg) BW were used in a 28-d study. Piglets were fed a common non-medicated diet for 7 d of acclimation. Treatments were arranged in a 2 × 2 factorial design with main effects of added Cu (0 vs. 200 mg/kg Cu from Cu sulfate) and chlortetracycline (0 vs. 440 mg/kg CTC). Growth performance and fecal samples were obtained on days 0, 14, and 28. There was no evidence (P > 0.05) for Cu and CTC interaction in growth performance. Pigs fed diets with added Cu had increased (P < 0.05) ADG and ADFI from days 0 to 14, with no evidence for differences (P > 0.05) from days 15 to 28 and 0 to 28. Pigs fed diets with CTC had improved (P < 0.01) ADG, ADFI, and G:F from days 0 to 28. Prevalence of tcrB-positive enterococci was not affected by the addition of Cu and/or CTC (P > 0.05). Prevalence of tcrB-positive enterococci was higher on day 14 than other sampling days (P = 0.002). Prevalence of tetracycline resistance gene [tet(M)]-positive enterococci was not affected by treatments or day (P > 0.05). Prevalence of macrolide resistance gene [erm(B)]-positive enterococci had a significant treatment and sampling day interaction (P = 0.021). The abundance of the tcrB gene in feces, quantified by PCR, was not affected by Cu treatment. The median Cu minimum inhibitory concentrations (MIC) of tcrB-negative and -positive isolates were 3 and 20 mM, respectively (P < 0.001). For day 0 and day 28, all Enterococcus isolates were susceptible to gentamicin, kanamycin, streptomycin, daptomycin, and tigecycline, with a majority of isolates resistant to chloramphenicol, erythromycin, lincomycin, linezolid, tetracycline, tylosin tartrate, and Synercid. In conclusion, 200 mg/kg added Cu or 440 mg/kg CTC in nursery diets improved growth performance of nursery pigs. Added Cu, with or without a selection pressure of CTC, did not increase Cu-resistant enterococci and did not co-select resistance to antibiotics.

A review of compensatory growth following lysine restriction in grow-finish pigs

Compensatory growth induced by lysine (Lys) restriction in grow-finish pigs is a complex physiological process affected by many factors and interactions, principally genotype, stage of growth at restriction, nature of nutritional restriction, and patterns of restriction and recovery. The scarcity of standard comparisons across the literature has hindered the characterization of important determinants of compensatory growth. Therefore, the present publication aims to review the current state of knowledge on compensatory growth induced by Lys restriction in grow-finish pigs, develop a database from peer-reviewed literature to standardize comparisons to characterize the occurrence of compensatory growth, and provide practical considerations for compensatory growth under field conditions. The literature search focused on publications directly or indirectly evaluating compensatory growth by having a period of Lys restriction followed by a recovery period of Lys sufficiency for grow-finish pigs. The database included 14 publications and 57 comparisons expressed as relative differences of restricted pigs compared to nonrestricted pigs. The database analysis described compensatory growth into complete, incomplete, and no compensatory growth categories and characterized the patterns of restriction and recovery in each category. The review of literature and database analysis supports the occurrence of compensatory growth induced by Lys restriction in grow-finish pigs. The degree of Lys restriction and duration of restriction and recovery periods seem to be critical in explaining differences between complete and incomplete compensatory growth, whereas Lys level in the recovery period seems to be critical between incomplete or no compensatory growth. Compensatory growth seems to be more likely if: 1) the degree of Lys restriction is between 10% and 30%; 2) Lys restriction is induced before pigs reach their maximum protein deposition; 3) duration of Lys restriction is short (maximum 40–45% overall duration) and duration of recovery period is long (minimum 55–60% overall duration); and 4) Lys level in recovery is close to or above the estimated requirements. In addition, compensatory growth can occur under commercial conditions and there seems to be an opportunity to exploit compensatory growth in grow-finish pigs to reduce feed cost and improve feed efficiency under certain market conditions.

Phase-feeding strategies based on lysine specifications for grow-finish pigs1

Four experiments were conducted using 1,100 to 1,188 pigs each (PIC 359 × 1,050) from ~27 to 127 kg BW to evaluate phase-feeding strategies based on Lys specifications and number of dietary phases for grow-finish pigs. Different phase-feeding strategies were used in each experiment with treatments consisting of a combination of 3 Lys specifications at 96%, 98%, or 100% of estimated requirement for growth rate and 4 phase-feeding strategies with 1, 2, 3, or 4 dietary phases. A single-phase-feeding strategy reduced (P < 0.05) overall growth performance, live BW, and HCW whether Lys specifications were at 98% or 100% of estimated requirements compared with multi-phase-feeding strategies. Lysine specifications at 96% of estimated requirements in a 4-phase-feeding strategy reduced (P < 0.05) overall growth performance compared with feeding strategies with Lys at 100% of estimated requirements, unless Lys specifications were increased to 100% of estimated requirements in the late finishing phase. Lysine specifications at 98% or 100% of estimated requirements in a 2-, 3- or 4-phase feeding strategy led to similar (P < 0.05) overall growth rate, live BW, and HCW of grow-finish pigs. Pigs fed 1, 2, or 3-phase feeding strategies or feeding strategies with Lys below the requirements in early grow finish had improved growth performance driven by improved feed efficiency in the period following low Lys levels, indicating the occurrence of compensatory growth. For carcass characteristics, there was no evidence (P > 0.10) for differences in carcass yield, back fat, loin depth, or lean percentage across feeding strategies in any of the experiments. In conclusion, phase-feeding strategies provide performance advantages over feeding a single dietary phase throughout the grow-finish period. Simplification of feeding strategies from 4 to 3 or 2 dietary phases with Lys specifications at 98% to 100% of estimated requirements for growth rate does not compromise overall growth performance and carcass characteristics of grow-finish pigs from 27 to 127 kg BW. Although, using feeding programs with fewer dietary phases and Lys set slightly below the requirements can compromise growth performance if initial BW and feed intake in the grow-finish period are lower than expected.

Effects of Bacillus subtilis C-3102 on sow and progeny performance, fecal consistency, and fecal microbes during gestation, lactation, and nursery periods1,2

This study evaluated the effects of providing a dietary probiotic, Bacillus subtilis C-3102, to sows during gestation and lactation and to progeny after weaning on performance, fecal consistency, and fecal microbes. For the sow portion of the study, 29 sows and litters were used from day 30 of gestation until weaning. Sow treatments consisted of control diet or probiotic diet with B. subtilis C-3102 at 500,000 cfu/g of gestation feed and 1,000,000 cfu/g of lactation feed. For the nursery portion of the study, 358 weaned pigs, progeny of sows on study, were used in a 42-d nursery study. Nursery treatments consisted of control diet or probiotic diet with B. subtilis C-3102 and prebiotics at 500,000 cfu/g of nursery feed. Treatments were arranged in a split-plot design with sow treatment (control or probiotic diet) as main plot and nursery treatment (control or probiotic diet) as subplot. Performance, fecal consistency by fecal score method, and fecal microbes by isolation and enumeration method were assessed. In lactation, probiotic-fed sows tended (P = 0.057) to have increased feed intake, but it did not improve (P > 0.05) sow or litter performance in lactation. In the nursery, there were no (P > 0.10) interactions or main effects of sow or nursery treatments on overall growth performance. However, pigs born from control-fed sows had greater (P < 0.05) average daily gain, average daily feed intake, and body weight in late nursery than pigs born from probiotic-fed sows. Fecal score evaluation of nursing and nursery pigs indicated no influence (P > 0.05) of sow or nursery treatments on fecal consistency. Fecal microbial analysis revealed a modest modification in fecal microbial population by increasing (P < 0.05) the number of total Bacillus sp. in probiotic-fed sows and nursery pigs. Nursing piglets born from probiotic-fed sows carried over (P < 0.05) this modification in fecal microbial population preweaning. In conclusion, providing a probiotic based on B. subtilis C-3102 to sows during gestation and lactation and to progeny after weaning did not elicit noteworthy improvements in performance or fecal consistency, but there was a benefit on sow lactation feed intake. Fecal microbial analysis indicated a maternal-progeny intestinal microbiota relationship with pigs born from probiotic-fed sows displaying similar fecal microbial population as sows. However, pigs born from probiotic-fed sows demonstrated reduced growth rate and feed consumption in late nursery.

Regression analysis to predict the impact of dietary neutral detergent fiber on carcass yield in swine

Research has shown that carcass yield in swine is reduced when ingredients with high neutral detergent fiber (NDF) content. Carcass yield reduction from feeding high-fiber ingredients results from an increase in the weight of intestinal contents. NDF has been shown to result in the digestive contents to swell in the large intestine by absorbing water thus increasing the fecal volume in the large intestine. Considering the financial implications of changing carcass yield, the objective of this project was to develop a regression equation to estimate carcass yield from dietary NDF and strategies where high-NDF ingredients are taken out of the diet in the last dietary phases before slaughter (withdrawal period; WP). Data from 8 experiments (43 observations) originated from 6 journal articles and 1 technical memo were used to develop the regression equation. The WP of high NDF ingredients was either none or ranged from 5 to 63 d in the experiments. Treatment diets of each trial were reformulated to obtain dietary nutrient content using the NRC ingredient library (NRC, Nutrient requirements of swine. 11th ed, 2012). Composition of experimental diets was used to calculate dietary net energy, crude protein, crude fiber, NDF, and acid detergent fiber in the last two dietary phases. These dietary compositions along with the number of days of WP were used to develop regression equations. The model was determined using a step-wise selection procedure starting with guided forward selection through individual predictor variables, with a statistical significance at P < 0.05 used to determine inclusion of terms in the final model. The regression analysis showed that WP, NDF level in the dietary phase prior to the final phase (NDF1), NDF level in the last dietary phase before marketing (NDF2), and the interaction between NDF2 and WP were the most important variables in the dataset to predict carcass yield. The resulting regression equation was as follows: carcass yield, % = 0.03492 ± 0.02633 × WP (d) - 0.05092 ± 0.02862 × NDF1 (%) - 0.06897 ± 0.02931 × NDF2 (%) - 0.00289 ± 0.00216 × (NDF2 [%] × WP [d]) + 76.0769 ± 1.33730. In conclusion, high levels of NDF up to slaughter had a negative impact on carcass yield. Increasing the length of the WP improved carcass yield; however, the effect of WP was dependent on the level of NDF2. The equation herein provides a tool to estimate of the impact of dietary NDF on carcass yield.

Caracterização histológica e imuno-histoquímica das lesões de tuberculose em bovinos e de linfadenite granulomatosa em suínos

Mycobacterium sp. induz inflamação granuloma-tosa em diferentes espécies animais. Mycobacterium bovis e o complexo Mycobacterium avium são importantes patógenos de bovinos e suínos e podem causar infecção em humanos, principalmente imunossuprimidos. Perdas na produção, barreiras comerciais e prejuízos por condenação de carcaças em abatedouro/frigorífico estão atrelados à ocorrência dessas infecções, com prejuízos econômicos significativos. Foi realizado um estudo de casos diagnosticados como tuberculose em bovinos e linfadenite granulomatosa em suínos no Setor de Patologia Veterinária da Universidade Federal do Rio Grande do Sul (SPV-UFRGS) no período de janeiro de 2007 a dezembro de 2011. Dados referentes à raça, ao sexo, à idade e ao histórico clínico foram compilados dos livros de registro e analisados. As características histológicas das lesões em linfonodos e pulmões foram avaliadas em Hematoxilina-Eosina, com predomínio de células gigantes nas lesões de tuberculose bovina e de macrófagos epitelioides em suínos. As técnicas histoquímicas de Ziehl-Neelsen e Tricrômico de Masson foram utilizadas para evidenciar, respectivamente, bacilos álcool-ácido resistentes e tecido conjuntivo fibroso nas lesões. A técnica de imuno-histoquímica foi utilizada em aproximadamente 30% dos casos estudados de cada espécie, selecionados aleatoriamente, para a caracterização do infiltrado linfocítico. Foram utilizados os anticorpos anti-CD3 para a marcação de linfócitos T e anti-CD79αcy para a marcação de linfócitos B. Linfócitos T predominaram nas lesões em ambas as espécies, com diferença estatisticamente significativa entre as médias dos linfócitos T e linfócitos B. Foi usado o teste t pareado, com t=5,501 (p<0,001) nas lesões dos bovinos e t=5,826 (p<0,001) para as lesões de linfadenite dos suínos. Adicionalmente foram marcados macrófagos com o uso do anticorpo anti-CD68 para bovinos e anti-Lisozima para suínos. Além desses, o anticorpo policlonal anti-Mycobacterium tuberculosis foi utilizado para a detecção de bactérias do gênero Mycobacterium, com imunomarcação positiva em todos os casos e, nos casos dos suínos, houve marcação anti-Mycobacterium avium.

Canine papillomatosis: a retrospective study of 24 cases (2001-2011) and immunohistochemical characterization

A retrospective study of 24 cases of papillomas in dogs was performed from January 2001 to March 2011. Additionally, immunohistochemistry (IHC) was used to characterize and evaluate the samples. We found that disease was observed more in mixed breed dogs, ages ranging from 6 months to 10 years (mean 3.1 years), and there was no gender predilection. The main lesion sites were the skin (75%), lips (16.7%), and eyelids (8.3%). Upon histological evaluation, we observed papillary exophytic proliferation of squamous epithelium and papillary endophytic proliferation (inverted) in 87.5% and 12.5% of cases, respectively. The tumors were characterized by spinous layer hyperplasia (87.5%) with koilocytes (70.8%) and intranuclear pale basophilic inclusions bodies (8.3%), prominent granular layer with large amounts of keratohyalin granules (95.8%), and hyperkeratosis in the stratum corneum (100%). Positive immunostaining for Papillomavirus was found in 83.3% of cases, which were distributed between the granular layer and the stratum corneum. These findings indicate the following: that papillomas in dogs are caused by Papillomavirus, the viral cytopathic effect induces epithelial lesions, viral particles are found inside the cell nuclei, and inclusions bodies are rare.