Epistasis, core-genome disharmony, and adaptation in recombining bacteria

Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome and are frequently observed as tightly linked cassettes with major effects. By contrast, interspecific recombination in the core genome is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma, we take advantage of an exceptional model system, the common enteric pathogens Campylobacter jejuni and C. coli that are known for very high magnitude interspecies gene flow in the core genome. As expected, HGT does indeed disrupt co-adapted allele pairings, indirect evidence of negative epistasis. However, multiple HGT events enable recovery of the genome's co-adaption between introgressing alleles, even in core metabolism genes (e.g., formate dehydrogenase). These findings demonstrate that, even for complex traits, genetic coalitions can be decoupled, transferred, and independently reinstated in a new genetic background-facilitating transition between fitness peaks. In this example, the two-step recombinational process is associated with C. coli that are adapted to the agricultural niche.IMPORTANCEGenetic exchange among bacteria shapes the microbial world. From the acquisition of antimicrobial resistance genes to fundamental questions about the nature of bacterial species, this powerful evolutionary force has preoccupied scientists for decades. However, the mixing of genes between species rests on a paradox: 0n one hand, promoting adaptation by conferring novel functionality; on the other, potentially introducing disharmonious gene combinations (negative epistasis) that will be selected against. Taking an interdisciplinary approach to analyze natural populations of the enteric bacteria Campylobacter, an ideal example of long-range admixture, we demonstrate that genes can independently transfer across species boundaries and rejoin in functional networks in a recipient genome. The positive impact of two-gene interactions appears to be adaptive by expanding metabolic capacity and facilitating niche shifts through interspecific hybridization. This challenges conventional ideas and highlights the possibility of multiple-step evolution of multi-gene traits by interspecific introgression.

Effects of different levels of organic chromium and selenomethionine cocktails in broilers

Selenium (Se) is an essential trace mineral that plays an important role in physiological processes by regulating the antioxidant defense system and enhancing immunity. Chromium is an essential mineral involved in carbohydrate and lipid metabolism and also plays a role in maintaining normal insulin function. Based on these advantages, we hypothesized that the addition of selenomethionine (SeMet) and organic chromium (OC) to broiler diets would increase Se deposition, antioxidant capacity and immune response in meat. Therefore, this study analyzed the effects of OC and SeMet on growh performance, nutrients digestibility, blood profiles, intestinal morphology, meat quality characteristics, and taxonomic analysis of broilers. A total of 168 one-day-old broiler chicken (Arbor Acres) were randomly allotted to 3 groups based on the initial body weight of 37.33 ± 0.24 g with 7 replicate per 8 birds (mixed sex). The experiments period was 28 days. Dietary treatments were folloewd: Basal diets based on corn-soybean meal (CON), basal diet supplemented with 0.2 ppm OC and 0.2 ppm SeMet (CS4), and basal diet supplemented with 0.4 ppm OC and 0.4 ppm SeMet (CS8). Supplementation of OC and SeMet did not affect on growth performance, nutrient digestibility. However, CS8 supplementation increased in duodenum villus height and villus height : crypt depth, and increased in breast meat Se deposition. In addition, CS8 group showed higher uric acid and total antioxidant status than CON group. Taxonomic analysis at phylum level revealed that Proteobacteria and Firmicutes of CS4 and CS8 were lower than CON group. In genus level, the relative abundance of fecal Lactobacillus and Enterococcus of CS4 and CS8 groups were higher than CON group. In short, 0.4 ppm OC and 0.4 ppm SeMet supplementation to broiler diet supporitng positive gut microbiome change, also enhancing antioxidant capacity, and Se deposition in breast meat.

Nano-Sized Selenium Maintains Performance and Improves Health Status and Antioxidant Potential While Not Compromising Ultrastructure of Breast Muscle and Liver in Chickens

The poultry industry is looking for the most effective sources of selenium (Se) for commercial use. Over the past five years, nano-Se has attracted a great deal of attention in terms of its production, characterisation and possible application in poultry production. The objective of this study was to evaluate the effects of dietary levels of inorganic and organic Se, selenised yeast and nano forms of selenium on breast meat quality, liver and blood markers of antioxidants, the ultrastructure of tissue and the health status of chickens. A total of 300 one-day-old chicks Ross 308 were divided into 4 experimental groups, in 5 replications, with 15 birds per replication. Birds were fed the following treatments: a standard commercial diet containing inorganic Se in the form of inorganic Se at the level of 0.3 mg/kg diet and an experimental diet with an increased level of Se (0.5 mg/kg diet). The use of other forms of Se (nano-Se) versus sodium selenate significantly influences (p ≤ 0.05) a higher collagen content and does not impair physico-chemical properties in the breast muscle or the growth performance of the chickens. In addition, the use of other forms of selenium at an increased dose versus sodium selenate affected (p ≤ 0.01) the elongation of sarcomeres in the pectoral muscle while reducing (p ≤ 0.01) mitochondrial damage in hepatocytes and improving (p ≤ 0.05) oxidative indices. The use of nano-Se at a dose of 0.5 mg/kg feed has high bioavailability and low toxicity without negatively affecting the growth performance and while improving breast muscle quality parameters and the health status of the chickens.

Changes in lipids metabolism indices as a result of different form of selenium supplementation in chickens

Selenium is an essential element that is important for many metabolic processes. Feed components used in chicken nutrition, especially cereals, may be deficient in selenium, hence selenium supplementation is necessary. Taking into account the progress in breeding, and thus the higher demand of birds for this element, it seems obvious to investigate an increased selenium dose in the diet of chickens. The aim of the study was to evaluate the effect of feed enriched with different forms of selenium at an increased dose of 0.5 mg/kg feed on the profile and metabolism of fatty acids in the breast muscle and liver of chickens. The study was conducted on 300 Ross 308 chickens reared for 42 days under standard conditions. The control group received feed supplemented with sodium selenite at a dose of 0.3 mg/kg feed. The research groups received different forms of selenium (sodium selenate, selenised yeast, nano-selenium) at an increased dose of 0.5 mg/kg feed. The study showed that the administration of different forms of selenium in the feed affected its concentration in the breast muscle and liver (p ≤ 0.01). Nano-selenium was found to have a high bioavailability, but also a lower risk of toxicity compared to other forms of selenium. Using different forms of selenium (p ≤ 0.01) at a dose of 0.5 mg/kg feed can significantly modify the fatty acid profile, lipid and enzymatic indices of fatty acid metabolism in breast muscle and liver.

Factors Affecting Breast Myopathies in Broiler Chickens and Quality of Defective Meat: A Meta-Analysis

Fast-growing broiler chickens are subjected to breast myopathies such as white striping (WS), wooden breast (WB), and spaghetti meat (SM). Available studies about risk factors for myopathy occurrence often used flock data whereas a few reports evaluated chicken individual data. Thus, the present study aimed to elucidate the effect of growth and slaughter traits, besides sex and genotype on myopathy occurrence. Data were obtained from eight experimental trials, which used a total of 6,036 broiler chickens. Sex, genotype, daily weight gain, slaughter weight, and breast yield were evaluated as potential risk factors by logistic regression analyses. Then, the effects of myopathy and sex were evaluated on meat rheological traits (pH, colour, cooking losses and shear force). Based on a logistic regression, WS occurrence was associated with genotype, breast weight, and breast yield. Compared with chickens with intermediate breast weight and breast yield, higher odds of having WS were found in chickens with high breast weight (OR: 1.49) and yield (OR: 1.27), whereas lower odds were found in those with low breast weight (OR: 0.57) and yield (OR: 0.82). As for WB and SM, females had lower odds of having WB (OR: 0.55) and higher odds of showing SM (OR: 15.4) compared to males. In males, higher odds of having WB were found in chickens with a high daily weight gain (OR: 1.75) compared to those with an intermediate daily weight gain. In females, higher odds of having SM were associated to a high slaughter weight (OR: 2.10) while lower odds to a low slaughter weight (OR: 0.87). As for meat quality, only WB meat was clearly different for some technological and sensorial properties, which can play a major role also in meat processing. In conclusion, our analysis identified breast development as a potential risk factor for WS, while a high growth was the risk factor for WB and SM. A different probability of having WB or SM in females and male was found.

Nutritional Intervention Strategies Using Dietary Antioxidants and Organic Trace Minerals to Reduce the Incidence of Wooden Breast and Other Carcass Quality Defects in Broiler Birds

Wooden breast (WB) is a degenerative myopathy seen in modern broiler birds resulting in quality downgrade of breast fillets. Affected filets show increased toughness both before as well as after cooking and have decreased water holding capacity and marinade pick up compared to normal fillets. Although the exact etiology is unknown, the circulatory insufficiency and increased oxidative stress in the breast muscles of modern broiler birds could be resulting in damage and degeneration of muscle fibers leading to myopathies. Three independent experiments were conducted to evaluate the effect of various dietary interventions on the incidence of WB when birds are exposed to oxidative stress associated with feeding oxidized fat and mild heat stress. Feed additives such as dietary antioxidant [Ethoxyquin (ETX)], mineral methionine hydroxy analog chelate (MMHAC) of Zn, Cu, and Mn, and organic selenium (Org Se) were tested at recommended levels. In experiment 1, ETX reduced (P < 0.05) the incidence of severe WB induced by oxidized fat diet. The magnitude of improvement in percentage of normal (no WB) filets and reduction in muscle lipid peroxidation was greater (P < 0.05) when ETX and MMHAC were fed together as shown by experiment 2. In birds exposed to mild heat stress (Experiment 3), feeding MMHAC by itself reduced (P < 0.05) tissue damage by reducing incidence of tibial head lesions, skin scratches, breast blisters, in addition to increasing the incidence of normal (no WB) fillets. When MMHAC was combined with ETX and Org Se, further improvement (P < 0.05) in normal (no WB) filets was observed. In summary, under different oxidative stress conditions, dietary intervention programs that contain ETX, MMHA-Zn, -Cu, and -Mn and Org Se can improve performance and increase carcass integrity, reducing problems, such as WB, either independently or with additive effect. This effect is most likely attained by simultaneously improving the exogenous and endogenous antioxidant status, reducing oxidative stress, and improving tissue healing process of the bird.

Selenium source and level on performance, selenium retention and biochemical responses of young broiler chicks

Background

Selenium (Se) has been recognized as an essential micronutrient for nearly all forms of life. In recent decades, broiler responses to dietary Se supplemental levels and sources have received considerable attention. On environmental grounds, organic trace mineral utilization in practical broiler feeds has been defended due to its higher bioavailability. In such feeds, trace minerals are provided simultaneously in the same supplement as inorganic salts or organic chelates, a fact commonly ignored in assays conducted to validate organic trace mineral sources. The current assay aimed to investigate growth and biochemical responses, as well as Se retention of growing chicks fed diets supplemented with organic and inorganic Se levels and where the trace minerals (zinc, copper, manganese, and iron) were provided as organic chelates or inorganic salts according to Se source assessed. In so doing, a 2 × 5 factorial arrangement was used to investigate the effects of sodium selenite (SS) and selenium-yeast (SY) supplemented in feeds to provide the levels of 0, 0.08, 0.16, 0.24, and 0.32 mg Se/kg.

Results

Chicks fed selenium-yeast diets had body weight (BW), and average daily gain (ADG) maximized at 0.133 and 0.130 mg Se/kg, respectively. Both Se sources linearly increased (P < 0.05) the glutathione peroxidase (GSH-Px) activity in chick blood but higher values were observed in sodium selenite fed chicks (P < 0.05). Both Se sources influenced thyroid hormone serum concentrations (P < 0.05). Chicks fed SY exhibited greater retention of Se in the feathers (P < 0.05). Relative bioavailability of selenium yeast compared with SS for the Se content in carcass, feathers, total and Se retention were, 126, 116, 125 and 125%, respectively. SY supplementation resulted in lower liver Se concentration as Se supplementation increased (P < 0.05).

Conclusions

Based on performance traits, the supplemental level of organic Se as SY in organic trace minerals supplement to support the maximal growth of broiler chicks is 0.133 mg Se/kg.

Hypoxia further exacerbates woody breast myopathy in broilers via alteration of satellite cell fate

Woody breast (WB) condition has created a variety of challenges for the global poultry industry. To date, there are no effective treatments or preventative measures due to its unknown (undefined) etiology. Several potential mechanisms including oxidative stress, fiber-type switching, cellular damage, and altered intracellular calcium levels have been proposed to play a key role in the progression of the WB myopathy. In a previous study, we have shown that WB is associated with hypoxia-like status and dysregulated oxygen homeostasis. As satellite cells (SC) play a pivotal role in muscle fiber repair and remodeling under stress conditions, we undertook the present study to determine satellite cell fate in WB-affected birds when reared in either normoxic or hypoxic conditions. Modern random bred broilers from 2015 (n = 200) were wing banded and reared under standard brooding practices for the first 2 wk post-hatch. At 15 d, chicks were divided in 2 body weight-matched groups and reared to 6 wk in either control local altitude or hypobaric chambers with simulated altitude of 6,000 ft. Birds were provided ad libitum access to water and feed, according to the Cobb recommendations. At 6 wk of age, birds were processed and scored for WB, and breast samples were collected from WB-affected and unaffected birds for molecular analyses (n = 10/group). SCs were isolated from normal breast muscle, cultured in vitro, and exposed to normoxia or hypoxia for 2 h. The expression of target genes was determined by qPCR using 2^−∆∆Ct method. Protein distribution and expression were determined by immunofluorescence staining and immunoblot, respectively. Data were analyzed by the Student's t test with significance set at P < 0.05. Multiple satellite cell markers, myogenic factor (Myf)-5 and paired box (PAX)-7 were significantly decreased at the mRNA and protein levels in the breast muscle from WB-affected birds compared to their unaffected counterparts. Lipogenic-and adipogenic-associated factors (acetyl-CoA carboxylase, ACCα; fatty acid synthase, FASN, malic enzyme, ME; and ATP citrate lyase, ACLY) were activated in WB-affected birds. These data were supported by an in vitro study where hypoxia decreased the expression of Myf5 and Pax7, and increased that of ACCα, FASN, ME, and ACLY. Together, these data indicate that under hypoxic condition, SC change fate by switching from a myogenic to an adipogenic program, which explains at least partly, the etiology of the WB myopathy.

Progressive in vivo detection of wooden breast in broilers as affected by dietary energy and protein

Wooden breast (WB) myopathy was investigated in broilers fed varying energy and protein at early ages. Correlation analyses were conducted between echogenicity of ultrasound images (US) of breast muscle from live birds and WB after slaughter. A total of 1,000 Cobb 500 one-day-old male chicks were fed on five dietary programs with eight replicates of 25 birds each, in a completely randomized design. Control feeds (commercially used ME and ideally balanced amino acids) or low-density feeds (low EP, with reductions of 50 kcal/kg ME and 0.20% dig. Lys compared to the control) were formulated. Feeds were provided in different periods: 1 to 7 d, 8 to 14 d, 15 to 21 d or 22 to 28 d. All broilers were fed a common basal diet thereafter until 49 d. Images using US were obtained once a week from all individuals and WB scored from one slaughtered bird per replication (0, normal; 1, mild hardening in the upper breast muscle; 2; moderate hardening in the upper and/or lower breast muscle; 3, severe hardening; 4, severe hardening with hemorrhagic lesions and yellow fluid). Blood was collected for enzyme investigation from the weekly slaughtered bird. Broilers had lower BWG and higher FCR when fed low EP feeds, regardless of the period fed when compared to the control (P < 0.001). Growth compensation, however, occurred afterwards such that all birds presented similar performance at the end. At 14, 21, and 28 d, broilers previously fed low EP feeds had lower WB scores (P < 0.001) compared to birds fed the control; however, both groups presented increased WB scores after 28 d. Wooden breast was positively correlated with breast echogenicity at 21 d (r = 0.31), 28 d (r = 0.43), 35 d (r = 0.21) and 42 d (r = 0.39). In conclusion, dietary energy and protein affected the development of WB scores in broilers and breast US images can be used as an early predictor of WB.

Muscle Metabolome Profiles in Woody Breast-(un)Affected Broilers: Effects of Quantum Blue Phytase-Enriched Diet

Woody breast (WB) myopathy is significantly impacting modern broilers and is imposing a huge economic burden on the poultry industry worldwide. Yet, its etiology is not fully defined. In a previous study, we have shown that hypoxia and the activation of its upstream mediators (AKT/PI3K/mTOR) played a key role in WB myopathy, and supplementation of quantum blue (QB) can help to reduce WB severity via modulation of hypoxia-related pathways. To gain further insights, we undertook here a metabolomics approach to identify key metabolite signatures and outline their most enriched biological functions. Ultra performance liquid chromatography coupled with high resolution mass spectrometry (UPLC-HRMS) identified a total of 108 known metabolites. Of these, mean intensity differences at P < 0.05 were found in 60 metabolites with 42 higher and 18 lower in WB-affected compared to unaffected muscles. Multivariate analysis and Partial Least Squares Discriminant analysis (PLS-DA) scores plot displayed different clusters when comparing metabolites profile from affected and unaffected tissues and from moderate (MOD) and severe (SEV) WB muscles indicating that unique metabolite profiles are present for the WB-affected and unaffected muscles. To gain biologically related molecule networks, a stringent pathway analyses was conducted using IPA knowledge-base. The top 10 canonical pathways generated, using a fold-change -1.5 and 1.5 cutoff, with the 50 differentially abundant-metabolites were purine nucleotide degradation and de novo biosynthesis, sirtuin signaling pathway, citrulline-nitric oxide cycle, salvage pathways of pyrimidine DNA, IL-1 signaling, iNOS, Angiogenesis, PI3K/AKT signaling, and oxidative phosphorylation. The top altered bio-functions in term of molecular and cellular functions in WB-affected tissues included cellular development, cellular growth and proliferation, cellular death and survival, small molecular biochemistry, inflammatory response, free radical scavenging, cell signaling and cell-to-cell interaction, cell cycles, and lipid, carbohydrate, amino acid, and nucleic acid metabolisms. The top disorder functions identified were organismal injury and abnormalities, cancer, skeletal and muscular disorders, connective tissue disorders, and inflammatory diseases. Breast tissues from birds fed with high dose (2,000 FTU) of QB phytase exhibited 22 metabolites with significantly different levels compared to the control group with a clear cluster using PLS-DA analysis. Of these 22 metabolites, 9 were differentially abundant between WB-affected and unaffected muscles. Taken together, this study determined many metabolic signatures and disordered pathways, which could be regarded as new routes for discovering potential mechanisms of WB myopathy.

An in vivo evaluation of the effects of feed restriction regimens on wooden breast using ultrasound images as a predictive tool

1. Gradual feed restriction was applied to broilers in order to reduce growth rate and, as a consequence, gradually impacts wooden breast myopathy occurrence. Ultrasound (US) images of breast muscle in live birds were correlated with breast fillets presenting wooden breast characteristics (WB). 2. A total of 1800 Cobb × Cobb 500 slow-feathering male chicks were fed one of the six feed restriction treatments with 12 replicates of 25 birds each, in a completely randomised design. Birds were fed ad libitum or were pair-fed to 50%, 60%, 70%, 80% or 90% of normal ad libitum intakes from 8 to 49 d to provide a gradual reduction in growth rate. Ultrasound images were obtained weekly from all birds and, in parallel, one bird per pen was weekly slaughtered and the major breast muscle was weighed and WB graded as 0 (normal), 1 (mild hardening in the upper), 2 (moderate hardening in the upper and/or lower), 3 (severe hardening) and 4 (severe hardening with haemorrhagic lesions and yellow fluid). Blood was taken for analysis of enzymes related to muscle cell breakdown. 3. Feed restriction applied at 50%, 60%, 70%, 80% and 90% of the ad libitum feed intake (FI) resulted in decreased body weight gain (BWG; P ≤ 0.05). 4. From 21 to 49 d, the increasing feed restriction led to linear increases (P ≤ 0.05) in WB scores, fibre density as well as breast depth and breast echogenicity. Creatine kinase, lactate dehydrogenase and aspartate aminotransferase concentration decreased linearly when broilers were feed restricted (P ≤ 0.05). 5. Wooden breast was positively correlated with echogenicity at 21 d (r = 0.510), 28 (r = 0.531), 35 (r = 0.470), 42 (r = 0.430) and 49 d (r = 0.548) (P ≤ 0.001). The use of breast echogenicity can be an additional tool to early detect alterations related to wooden breast.

Maternal Selenium and Developmental Programming

Selenium (Se) is an essential trace element of fundamental importance to health due to its antioxidant, anti-inflammatory, and chemopreventive properties, attributed to its presence within at least 25 selenoproteins (Sel). In this review, we describe some of the recent progress, in our understanding, on the impact of maternal Se intake during the periconceptional period on offspring development and health. Maternal nutrition affects the performance and health of the progeny, and both maternal and offspring Se supplementations are essential for the optimal health and antioxidant protection of the offspring. The case of Se in epigenetic programming and early life nutrition is also discussed.

Wooden-Breast, White Striping, and Spaghetti Meat: Causes, Consequences and Consumer Perception of Emerging Broiler Meat Abnormalities

Ten years ago, the occurrence of macroscopic defects in breasts muscles from fast-growing broilers challenged producers and animal scientists to label and characterize myopathies wholly unknown. The distinctive white striations in breasts affected by white striping disorder, the presence of out-bulging and pale areas of hardened consistency in the so-called wooden breast, and the separation of the fiber bundles in breasts labelled as spaghetti meat, made these myopathies easily identified in chicken carcasses. Yet, the high incidence of these myopathies and the increasing concern by producers and retailers led to an unprecedented flood of questions on the causes and consequences of these abnormal chicken breasts. This review comprehensively collects the most relevant information from studies aimed to understand the pathological mechanisms of these myopathies, their physicochemical and histological characterization and their impact on meat quality and consumer's preferences. Today, it is known that the occurrence is linked to fast-growth rates of the birds and their large breast muscles. The muscle hypertrophy along with an unbalanced growth of supportive connective tissue leads to a compromised blood supply and hypoxia. The occurrence of oxidative stress and mitochondrial dysfunction leads to lipidosis, fibrosis, and overall myodegeneration. Along with the altered appearance, breast muscles affected by the myopathies display poor technological properties, impaired texture properties, and reduced nutritional value. As consumer's awareness on the occurrence of these abnormalities and the concerns on animal welfare arise, efforts are made to inhibit the onset of the myopathies or alleviate the severity of the symptoms. The lack of fully effective dietary strategies leads scientists to propose whether "slow" production systems may alternatively provide with poultry meat free of these myopathies.

The Incidence of Muscle Abnormalities in Broiler Breast Meat - A Review

The dramatic improvements in the growth rate and breast muscle size and yield in broilers through the intensive genetic selection, and the improvement in nutrition and management over the past 50 years have introduced serious abnormalities that influenced the quality of breast meat. The abnormalities include pale-soft-exudative (PSE) conditions, deep pectoral muscle (DPM) myopathy, spaghetti meat (SM), white striping (WS), and woody breast (WB) that have serious negative implications to the broiler meat industry. The incidences of PSE and DPM have been known for several decades, and their prevalence, etiology and economic impact have been well discussed. However, other abnormalities such as SM, WS and WB conditions have been reported just for few years although these conditions have been known for some time. The newly emerging quality issues in broilers are mainly associated with the Pectoralis major muscles, and the incidences have been increased dramatically in some regions of the world in recent years. As high as 90% of the broilers are affected by the abnormalities, which are expected to cause from $200 million to $1 billion economic losses to the U.S. poultry industry per year. So, this review mainly discusses the histopathological characteristics and biochemical changes in the breast muscles with the emphasis on the newly emerging abnormalities (SM, WS, and WB) although other abnormalities are also discussed. The impacts of the anomalies on the nutritional, functional, mechanical and sensory quality of the meat and their implications to the poultry industry are discussed.