An insight into the commercial piglet's microbial gut colonization: from birth towards weaning.

BACKGROUND: The establishment of the gut microbiota can be influenced by several perinatal factors, including, most importantly, the maternal microbiota. Moreover, early-life environmental variation affects gut microbial colonization and the intestinal health of offspring throughout life. The present study aimed to explore the development of piglet gut microbiota from birth to weaning in the commercial practice and also to assess how different farm environments could condition this process. Although it is possible to find in the literature other studies with similar objectives this work probably represents one of the few studies that make a systematic evaluation of such differential factors under a real scenario. To achieve this objective, we performed two trials. In a first Trial, we selected 2 farms in which we performed an intensive sampling (5 samples /animal) to characterize the gut colonization pattern during the first days of life and to identify the time window with the greatest impact. Both farms differed in their health status and the use of antimicrobials in the piglets. In a second Trial, we selected 4 additional farms with variable rearing conditions and a distinctive use of antimicrobials in the sows with a simplified sampling pattern (2 samples/animal). Faecal samples were obtained with swabs and DNA was extracted by using the PSP® Spin Stool DNA Kit and sequencing of the 16S rRNA gene (V3-V4 region) performed by Illumina MiSeq Platform. RESULTS: The present study contributes to a better understanding of microbiome development during the transition from birth to weaning in commercial conditions. Alpha diversity was strongly affected by age, with an increased richness of species through time. Beta diversity decreased after weaning, suggesting a convergent evolvement among individuals. We pinpointed the early intestinal colonizers belonging to Bacteroides, Escherichia-Shigella, Clostridium sensu stricto 1, and Fusobacterium genera. During lactation(d7-d21 of life), the higher relative abundances of Bacteroides and Lactobacillus genera were correlated with a milk-oriented microbiome. As the piglets aged and after weaning (d36 of life), increasing abundances of genera such as Prevotella, Butyricimonas, Christensenellaceae R-7 group, Dorea, Phascolarctobacterium, Rikenellaceae RC9 gut group, Subdoligranulum, and Ruminococcaceae UCG-002 were observed. These changes indicate the adaptation of the piglets to a cereal-based diet rich in oligosaccharides and starch. Our results also show that the farm can have a significant impact in such a process, evidencing the influence of different environments and rearing systems on the gut microbiota development of the young piglet. Differences between farms were more noticeable after weaning than during lactation with changes in alpha and beta biodiversity and specific taxa. The analysis of such differences suggests that piglets receiving intramuscular amoxicillin (days 2-5 of life) and being offered an acidifying rehydrating solution (Alpha farm in Trial 1) have a greater alpha diversity and more abundant Lactobacillus population. Moreover, the only farm that did not offer any rehydrating solution (Foxtrot farm in Trial 2) showed a lower alpha diversity (day 2 of life) and increased abundance of Enterobacteriaceae (both at 2 and 21 days). The use of in-feed antibiotics in the sows was also associated with structural changes in the piglets' gut ecosystem although without changes in richness or diversity. Significant shifts could be registered in different microbial groups, particularly lower abundances of Fusobacterium in those piglets from medicated sows. CONCLUSIONS: In conclusion, during the first weeks of life, the pig microbiota showed a relevant succession of microbial groups towards a more homogeneous and stable ecosystem better adapted to the solid dry feed. In this relevant early-age process, the rearing conditions, the farm environment, and particularly the antimicrobial use in piglets and mothers determine changes that could have a relevant impact on gut microbiota maturation. More research is needed to elucidate the relative impact of these farm-induced early life-long changes in the growing pig.

How copper can impact pig growth: comparing the effect of copper sulfate and monovalent copper oxide on oxidative status, inflammation, gene abundance, and microbial modulation as potential mechanisms of action.

The beneficial effect of elevated concentrations of copper (Cu) on growth performance of pigs has been already demonstrated; however, their mechanism of action is not fully discovered. The objective of the present experiment was to investigate the effects of including Cu from copper sulfate (CuSO4) or monovalent copper oxide (Cu2O) in the diet of growing pigs on oxidative stress, inflammation, gene abundance, and microbial modulation. We used 120 pigs with initial body weight (BW) of 11.5 ± 0.98 kg in 2 blocks of 60 pigs, 3 dietary treatments, 5 pigs per pen, and 4 replicate pens per treatment within each block for a total of 8 pens per treatment. Dietary treatments included the negative control (NC) diet containing 20 mg Cu/kg and 2 diets in which 250 mg Cu/kg from CuSO4 or Cu2O was added to the NC. On day 28, serum samples were collected from one pig per pen and this pig was then euthanized to obtain liver samples for the analysis of oxidative stress markers (Cu/Zn superoxide dismutase, glutathione peroxidase, and malondialdehyde, MDA). Serum samples were analyzed for cytokines. Jejunum tissue and colon content were collected and used for transcriptomic analyses and microbial characterization, respectively. Results indicated that there were greater (P < 0.05) MDA levels in the liver of pigs fed the diet with 250 mg/kg CuSO4 than in pigs fed the other diets. The serum concentration of tumor necrosis factor-alpha was greater (P < 0.05) in pigs fed diets containing CuSO4 compared with pigs fed the NC diet or the diet with 250 mg Cu/kg from Cu2O. Pigs fed diets containing CuSO4 or Cu2O had a greater (P < 0.05) abundance of genes related to the intestinal barrier function and nutrient transport, but a lower (P < 0.05) abundance of pro-inflammatory genes compared with pigs fed the NC diet. Supplementing diets with CuSO4 or Cu2O also increased (P < 0.05) the abundance of Lachnospiraceae and Peptostreptococcaceae families and reduced (P < 0.05) the abundance of the Rikenellaceae family, Campylobacter, and Streptococcus genera in the colon of pigs. In conclusion, adding 250 mg/kg of Cu from CuSO4 or Cu2O regulates genes abundance in charge of the immune system and growth, and promotes changes in the intestinal microbiota; however, Cu2O induces less systemic oxidation and inflammation compared with CuSO4.

Copper is a nonrenewable mineral resource that is essential for all biological organisms. After banning the antibiotics, copper has received considerable attention due to its antimicrobial properties that improve performance in animals when fed over the minimum requirement. The present study evaluated two sources of Cu (copper sulfate and monovalent copper oxide) compared with a nonsupplemented diet and the likely mechanism of action which leads to improved pig performance. Pigs fed high concentrations of copper sulfate showed increased liver oxidation and inflammatory indicators in the blood. Elevated concentrations of Cu improved intestinal epithelial barrier function, modulation of inflammatory responses, increased beneficial microbes, and reduced pathogens in the gut. Therefore, supplementation of high levels of Cu appears to be effective in promoting pig growth, but therapeutic doses of Cu sulfate increase the inflammatory response.

Body weight of newborn and suckling piglets affects their intestinal gene expression.

Modern hyperprolific sows must deal with large litters (16-20 piglets) which reduce piglet birthweight with a concomitant increase in the proportion of small and intrauterine growth retarded piglets. However, larger litters do not only have a greater variation of piglet weights, but also a greater variation in colostrum and milk consumption within the litter. To further understand the impact that body weight has on piglets, the present study aimed to evaluate the degree of physiological weakness of the smallest piglets at birth and during the suckling period (20 d) compared to their middle-weight littermates through their jejunal gene expression. At birth, light piglets showed a downregulation of genes related to immune response (FAXDC2, HSPB1, PPARGC1α), antioxidant enzymes (SOD2m), digestive enzymes (ANPEP, IDO1, SI), and nutrient transporter (SLC39A4) (P < 0.05) but also a tendency for a higher mRNA expression of GBP1 (inflammatory regulator) and HSD11ß1 (stress hormone) genes compared to their heavier littermates (P < 0.10). Excluding HSD11ß1 gene, all these intestinal gene expression differences initially observed at birth between light and middle-weight piglets were stabilized at the end of the suckling period, when others appeared. Genes involved in barrier function (CLDN1), pro-inflammatory response (CXCL2, IL6, IDO1), and stress hormone signaling (HSD11ß1) over-expressed compared to their middle-weight littermates (P < 0.05). In conclusion, at birth and at the end of suckling period, light body weight piglets seem to have a compromised gene expression and therefore impaired nutrient absorption, immune and stress responses compared to their heavier littermates.

Under hyperprolific situations, piglets must deal with a reduced birthweight and a severe sibling competition for nutrients. Therefore, light body weight newborn and suckling piglets may also have physiological disadvantages compared to their middle-weight littermates. To further understand the impact that body weight has on piglets, the present study aimed to evaluate the degree of physiological weakness of the smallest piglets at birth and during the suckling period (20 d) compared to their middle-weight littermates through their jejunal gene expression. Newborn light piglets downregulated genes related to immunity, antioxidant, and digestive activities, but also a tendency to upregulate other genes related to inflammation and stress responses. At the end of the suckling period, those genes expression differences vanished while others appear. Light weight piglets showed lower expression of genes involved in barrier function, inflammation, and stress responses compared to their middle-weight littermates. At birth and at the end of lactation, light piglets seem to have a compromised intestinal gene expression for nutrient absorption, immune and stress responses compared to their heavier littermates.

Potential effect of two Bacillus probiotic strains on performance and fecal microbiota of breeding sows and their piglets.

The effect of long-term administration of two Bacillus strains was tested on 98 breeding sows and their litters allotted into three treatments: a control group (CON); supplemented with 5 × 108 cfu/kg B. subtilis - 541 (BSU); or with 5 × 108 cfu/kg B. amyloliquefaciens - 516 (BAM). Reproductive and performance variables were recorded over three cycles with 56 dams remaining through the third lactation. Blood and fecal samples were taken longitudinally from 12 sows per treatment on days 8 and 21 of the third lactation and milk samples were taken on day 21. Feces from one piglet per litter was sampled on days 21 and 33 and jejunal gene expression was assessed in two piglets on day 21. Changes in fecal microbiota were assessed by 16S rRNA gene sequencing (Illumina MiSeq) and gene expression by Open-Array technology. Metabolomic responses were analyzed in milk by NMR and Ig-G and Ig-A specific antibodies were determined by ELISA. No significant differences were observed on feed intake, body weight, or fat mobilization of the sows. However, a significant increase in the total number of piglets born was observed in supplemented sows. Although the increase was seen from the first cycle with BAM, improvements were not seen with BSU until the third cycle. BAM also increased the number of born-alive and weaned piglets. NMR analysis showed an impact of BAM on milk composition. No differences were found in milk or blood immunoglobulins. A different structure of the fecal microbiota was found in supplemented sows, with changes across phylum, family, and genus. These changes were greater at day 8, suggesting a relevant role of probiotics establishing a new intestinal balance after labor. Shifts in the microbiota were also seen in the piglets, with a clearer impact post-weaning than in suckling. In this regard, correlations between microbial groups of sows and piglets showed a higher link with weaned (d33) than with suckling pigs (d21), reinforcing the idea of an early maternal carry-over. No changes due to treatment in jejunal gene expression were detected; however, piglet size had a clear impact on different genes. In summary, the addition of both probiotics, and particularly Bacillus amyloliquefaciens, demonstrated potential benefits on the prolificacy of sows. Daily feeding of Bacillus amyloliquefaciens resulted in an increase in the number of weaned piglets. The high correlations between the compositions of the microbiota of sows and their piglets are evidence of maternal imprinting, with effects lasting beyond weaning.

The aim of the present study was to determine if the inclusion of probiotic microorganisms in the mother's diet during gestation and the lactation period is capable of modifying the performance of mothers and piglets and the possible effect on the intestinal health of piglets after separation from the mother. For this, 98 females were distributed in three experimental treatments: a control diet, or the same diet in which one of two probiotic strains to be tested (Bacillus subtilis or Bacillus amyloliquefaciens) were incorporated. The experimental diets were administered during pregnancy and the lactation phase for three consecutive productive cycles. Among the most striking results, it is worth highlighting the impact of probiotic treatments on the reproductive performance of sows. Both supplemented groups showed a higher number of total piglets per sow. Furthermore, sows that received the Bacillus amyloliquefaciens diet showed a significant increase in the number of live-born piglets. Probiotic supplementation also showed effects on the fecal microbiota composition of the mothers and their piglets. Changes in the composition of sow milk were also observed. In summary, results demonstrated the potential benefits of supplementing probiotics, and particularly a strain of Bacillus amyloliquefaciens, to improve prolificacy, modulate the intestinal microbial composition, and improve the performance of piglets during lactation.

Effectiveness of Two Plant-Based In-Feed Additives against an Escherichia coli F4 Oral Challenge in Weaned Piglets.

This study evaluates the efficacy of two plant-based feed supplementations to fight colibacillosis in weanlings. A total of 96 piglets (32 pens) were assigned to four diets: a control diet (T1) or supplemented with ZnO (2500 ppm Zn) (T2) or two different plant supplements, T3 (1 kg/t; based on essential oils) and T4 (T3 + 1.5 kg/t based on non-volatile compounds). After one week, animals were challenged with ETEC F4, and 8 days after, one animal per pen was euthanized. Performance, clinical signs, microbial analysis, inflammatory response, intestinal morphology, and ileal gene expression were assessed. ZnO improved daily gains 4 days after challenge, T3 and T4 showing intermediate values (96, 249, 170, and 157 g/d for T1, T2, T3, and T4, p = 0.035). Fecal lactobacilli were higher with T3 and T4 compared to ZnO (7.55, 6.26, 8.71, and 8.27 cfu/gFM; p = 0.0007) and T3 increased the lactobacilli/coliforms ratio (p = 0.002). T4 was associated with lower levels of Pig-MAP (p = 0.07) and increases in villus/crypt ratio (1.49, 1.90, 1.73, and 1.84; p = 0.009). Moreover, T4 was associated with an upregulation of the REG3G gene (p = 0.013; pFDR = 0.228) involved in the immune response induced by enteric pathogens. In conclusion, both plant supplements enhanced animal response in front of an ETEC F4 challenge probably based on different modes of action.

Strategies of inorganic and organic trace mineral supplementation in gestating hyperprolific sow diets: effects on the offspring performance and fetal programming.

The aim of the present study was to evaluate the effect of trace mineral nutrition on sow performance, mineral content, and intestinal gene expression of neonate piglets when inorganic mineral sources (ITM) were partially replaced by their organic mineral (OTM) counterparts. At 35 d postmating, under commercial conditions, a total of 240 hyperprolific multiparous sows were allocated into three experimental diets: 1) ITM: with Zn, Cu, and Mn at 80, 15, and 60 mg/kg, respectively; 2) partial replacement trace mineral source (Replace): with a 30 % replacement of ITM by OTM, resulting in ITM + OTM supplementation of Zn (56 + 24 mg/kg), Cu (10.5 + 4.5 mg/kg), and Mn (42 + 18 mg/kg); and 3) Reduce and replace mineral source (R&R): reducing a 50% of the ITM source of Zn (40 + 24 mg/kg), Cu (7.5 + 4.5 mg/kg), and Mn (30 + 18 mg/kg). At farrowing, 40 piglets were selected, based on birth weight (light: <800 g, and average: >1,200 g), for sampling. Since the present study aimed to reflect results under commercial conditions, it was difficult to get an equal parity number between the experimental diets. Overall, no differences between experimental diets on sow reproductive performance were observed. Light piglets had a lower mineral content (P < 0.05) and a downregulation of several genes (P < 0.10) involved in physiological functions compared with their average littermates. Neonate piglets born from Replace sows had an upregulation of genes involved in functions like immunity and gut barrier, compared with those born from ITM sows (P < 0.10), particularly in light piglets. In conclusion, the partial replacement of ITM by their OTM counterparts represents an alternative to the totally inorganic supplementation with improvements on neonate piglet gene expression, particularly in the smallest piglets of the litter. The lower trace mineral storage together with the greater downregulation of gut health genes exposed the immaturity and vulnerability of small piglets.

Targeted-Release Organic Acids and Essential Oils Improve Performance and Digestive Function in Broilers Under a Necrotic Enteritis Challenge.

An experiment was performed to evaluate the effect of four different microencapsulated blends of organic acids (OA) and nature-identical aromatic compounds (AC) on growth performance and gut health of broilers challenged with a recycled NE litter. A total of 600 one-day-old male Ross 308 broilers were randomly assigned to five treatments consisting of a basal diet (as negative control) supplemented with each of the tested microencapsulated blends: OA1 (malic and fumaric acid) + AC; 2.5 g/kg; OA2 (calcium butyrate+fumaric acid) + AC; 1.7 g/kg; MCFA (capric-caprylic; caproic and lauric acid) + AC; 2 g/kg; and MCFA + OA3(calcium butyrate + fumaric and citric acid) + AC; 1.5 g/kg. The AC used was the same for all treatments; including cinnamaldehyde, carvacrol, and thymol (8:1:1), as major compounds. Three tested blends enhanced growth performance by improving intestinal histomorphology (p < 0.001). The tested blends enhanced the abundance of some beneficial families such as Ruminococcaceae and Lachnospiraceae; while reducing that of harmful ones such as Enterobacteriaceae and Helicobacteraceae. A further dose-response experiment showed that 0.5 g/kg of the blend 2 and 2 g/kg of the blend 4 improved growth performance and intestinal histomorphology of chickens on d 42 and decreased fecal Enterobacteriaceae and C. perfringens counts. Similar effects to the previous experiment were observed for cecum microbiota.

Diversity of volatile organic compound production from leucine and citrate in Enterococcus faecium.

Enterococcus faecium is frequently isolated from fermented food; in particular, they positively contribute to the aroma compound generation in traditional cheese. Citrate fermentation is a desirable property in these bacteria, but this feature is not uniformly distributed among E. faecium strains. In the present study, three selected E. faecium strains, IQ110 (cit-), GM70 (cit+ type I), and Com12 (cit+ type II), were analyzed in their production of aroma compounds in milk. End products and volatile organic compounds (VOCs) were determined by solid-phase micro-extraction combined with gas chromatography mass spectrometry (SPME-GC-MS). Principal component analysis (PCA) of aroma compound profiles revealed a different VOC composition for the three strains. In addition, resting cell experiments of E. faecium performed in the presence of leucine, citrate, or pyruvate as aroma compound precursors allowed us to determine metabolic differences between the studied strains. GM70 (cit+ type I) showed an active citrate metabolism, with increased levels of diacetyl and acetoin generation relative to Com12 or to citrate defective IQ110 strains. In addition, in the experimental conditions tested, a defective citrate-fermenting phenotype for the Com12 strain was found, while its leucine degradation and pyruvate metabolism were conserved. In conclusion, rational selection of E. faecium strains could be performed based on genotypic and phenotypic analyses. This would result in a performing strain, such as GM70, that could positively contribute to flavor, with typical notes of diacetyl, acetoin, 3-methyl butanal, and 3-methyl butanol in an adjuvant culture.

Fruit metabolic and transcriptional programs differentiate among Andean tomato (Solanum lycopersicum L.) accessions.

MAIN CONCLUSION: Andean tomatoes differed from the wild ancestor in the metabolic composition and the expression of genes related with mitochondrial functions, and environmental stresses, making them potentially suitable for breeding programmes. Traditional landraces or "criollo" tomatoes (Solanum lycopersicum L.) from Andean areas of Argentina, selected for their fruit quality, were analysed in this study. We explored the metabolome and transcriptome of the ripe fruit in nine landrace accessions representing the seven genetic groups and compared them to the mature fruit of the wild progenitor Solanum pimpinellifolium. The content of branched- (isoleucine and valine) and aromatic (phenylalanine and tryptophan) amino acids, citrate and sugars were significantly different in the fruit of several "criollo" tomatoes compared to S. pimpinellifolium. The transcriptomic profile of the ripe fruit showed several genes significantly and highly regulated in all varieties compared to S. pimpinellifolium, like genes encoding histones and mitochondrial proteins. Additionally, network analysis including transcripts and metabolites identified major hubs with the largest number of connections such as constitutive photomorphogenic protein 1 (a RING finger-type ubiquitin E3 ligase), five Zn finger transcription factors, ascorbate peroxidase, acetolactate synthase, and sucrose non-fermenting 1 kinase. Co-expression analysis of these genes revealed a potential function in acquiring tomato fruit quality during domestication.

Contrasting metabolic profiles of tasty Andean varieties of tomato fruit in comparison with commercial ones.

BACKGROUND: The fruits of most commercial tomato cultivars (Solanum lycopersicum L.) are deficient in flavour. In contrast, traditional 'criollo' tomato varieties are appreciated for fruit of excellent organoleptic quality. Small farmers from the Andean valleys in Argentina have maintained their own tomato varieties, which were selected mainly for flavour. This work aims to correlate the chemical composition of the fruit with the sensory attributes of eight heirloom tomato varieties. The long-term goal is to identify potential candidate genes capable of altering the chemicals involved in flavour. RESULTS: A sensory analysis was conducted and the metabolomics of fruit were determined. The data revealed that defined tomato aroma and sourness correlated with citrate and several volatile organic compounds (VOC), such as α-terpineol, p-menth-1-en-9-al, linalool and 3,6-dimethyl-2,3,3a,4,5,7a-hexahydrobenzofuran (DMHEX), a novel volatile recently identified in tomato. Two sensory attributes - sweetness and a not-acidic taste - correlated with the characteristic tomato taste, and also with fructose, glucose, and two VOCs, benzaldehyde, and 2-methyl-2-octen-4-one. CONCLUSIONS: These data provide new evidence of the complex chemical combination that induced the flavour and aroma of the good-tasting 'criollo' tomato fruit. That is, the compounds that correlated with defined tomato aroma and acidic taste did not correlate with sweetness, or with characteristic tomato taste. © 2018 Society of Chemical Industry.

Reduced levels of NADH-dependent glutamate dehydrogenase decrease the glutamate content of ripe tomato fruit but have no effect on green fruit or leaves.

Glutamate (Glu) is a taste enhancer that contributes to the characteristic flavour of foods. In fruit of tomato (Solanum lycopersicum L.), the Glu content increases dramatically during the ripening process, becoming the most abundant free amino acid when the fruit become red. There is also a concomitant increase in NADH-dependent glutamate dehydrogenase (GDH) activity during the ripening transition. This enzyme is located in the mitochondria and catalyses the reversible amination of 2-oxoglutarate to Glu. To investigate the potential effect of GDH on Glu metabolism, the abundance of GDH was altered by artificial microRNA technology. Efficient silencing of all the endogenous SlGDH genes was achieved, leading to a dramatic decrease in total GDH activity. This decrease in GDH activity did not lead to any clear morphological or metabolic phenotype in leaves or green fruit. However, red fruit on the transgenic plants showed markedly reduced levels of Glu and a large increase in aspartate, glucose and fructose content in comparison to wild-type fruit. These results suggest that GDH is involved in the synthesis of Glu in tomato fruit during the ripening processes. This contrasts with the biological role ascribed to GDH in many other tissues and species. Overall, these findings suggest that GDH has a major effect on the control of metabolic composition during tomato fruit ripening, but not at other stages of development.

FasR, a novel class of transcriptional regulator, governs the activation of fatty acid biosynthesis genes in Streptomyces coelicolor.

Membrane lipid homeostasis is essential for bacterial survival and adaptation to different environments. The regulation of fatty acid biosynthesis is therefore crucial for maintaining the correct composition and biophysical properties of cell membranes. This regulation implicates a biochemical control of key enzymes and a transcriptional regulation of genes involved in lipid metabolism. In Streptomyces coelicolor we found that control of lipid homeostasis is accomplished, at least in part, through the transcriptional regulation of fatty acid biosynthetic genes. A novel transcription factor, FasR (SCO2386), controls expression of fabDHPF operon and lies immediately upstream of fabD, in a cluster of genes that is highly conserved within actinomycetes. Disruption of fasR resulted in a mutant strain, with severe growth defects and a delay in the timing of morphological and physiological differentiation. Expression of fab genes was downregulated in the fasR mutant, indicating a role for this transcription factor as an activator. Consequently, the mutant showed a significant drop in fatty acid synthase activity and triacylglyceride accumulation. FasR binds specifically to a DNA sequence containing fabDHPF promoter region, both in vivo and in vitro. These data provide the first example of positive regulation of genes encoding core proteins of saturated fatty acid synthase complex.