Mycoplasma hyopneumoniae variability: Current trends and proposed terminology for genomic classification

Mycoplasma hyopneumoniae (M. hyopneumoniae) is the aetiologic agent of enzootic pneumonia in swine, a prevalent chronic respiratory disease worldwide. Mycoplasma hyopneumoniae is a small, self‐replicating microorganism that possesses several characteristics allowing for limited biosynthetic abilities, resulting in the fastidious, host‐specific growth and unique pathogenic properties of this microorganism. Variation across several isolates of M. hyopneumoniae has been described at antigenic, proteomic, transcriptomic, pathogenic and genomic levels. The microorganism possesses a minimal number of genes that regulate the transcription process. Post‐translational modifications (PTM) occur frequently in a wide range of functional proteins. The PTM by which M. hyopneumoniae regulates its surface topography could play key roles in cell adhesion, evasion and/or modulation of the host immune system. The clinical outcome of M. hyopneumoniae infections is determined by different factors, such as housing conditions, management practices, co‐infections and also by virulence differences among M. hyopneumoniae isolates. Factors contributing to adherence and colonization as well as the capacity to modulate inflammatory and immune responses might be crucial. Different components of the cell membrane (i.e. proteins, glycoproteins and lipoproteins) may serve as adhesins and/or be toxic for the respiratory tract cells. Mechanisms leading to virulence are complex and more research is needed to identify markers for virulence. The utilization of typing methods and complete or partial‐gene sequencing for M. hyopneumoniae characterization has increased in diagnostic laboratories as control and elimination strategies for this microorganism are attempted worldwide. A commonly employed molecular typing method for M. hyopneumoniae is Multiple‐Locus Variable number tandem repeat Analysis (MLVA). The agreement of a shared terminology and classification for the various techniques, specifically MLVA, has not been described, which makes inferences across the literature unsuitable. Therefore, molecular trends for M. hyopneumoniae have been outlined and a common terminology and classification based on Variable Number Tandem Repeats (VNTR) types has been proposed.info:eu-repo/semantics/acceptedVersio

Mycoplasma hyopneumoniae variability : current trends and proposed terminology for genomic classification

Mycoplasma hyopneumoniae (M. hyopneumoniae) is the aetiologic agent of enzootic pneumonia in swine, a prevalent chronic respiratory disease worldwide. Mycoplasma hyopneumoniae is a small, self-replicating microorganism that possesses several characteristics allowing for limited biosynthetic abilities, resulting in the fastidious, host-specific growth and unique pathogenic properties of this microorganism. Variation across several isolates of M. hyopneumoniae has been described at antigenic, proteomic, transcriptomic, pathogenic and genomic levels. The microorganism possesses a minimal number of genes that regulate the transcription process. Post-translational modifications (PTM) occur frequently in a wide range of functional proteins. The PTM by which M. hyopneumoniae regulates its surface topography could play key roles in cell adhesion, evasion and/or modulation of the host immune system. The clinical outcome of M. hyopneumoniae infections is determined by different factors, such as housing conditions, management practices, co-infections and also by virulence differences among M. hyopneumoniae isolates. Factors contributing to adherence and colonization as well as the capacity to modulate inflammatory and immune responses might be crucial. Different components of the cell membrane (i.e. proteins, glycoproteins and lipoproteins) may serve as adhesins and/or be toxic for the respiratory tract cells. Mechanisms leading to virulence are complex and more research is needed to identify markers for virulence. The utilization of typing methods and complete or partial-gene sequencing for M. hyopneumoniae characterization has increased in diagnostic laboratories as control and elimination strategies for this microorganism are attempted worldwide. A commonly employed molecular typing method for M. hyopneumoniae is Multiple-Locus Variable number tandem repeat Analysis (MLVA). The agreement of a shared terminology and classification for the various techniques, specifically MLVA, has not been described, which makes inferences across the literature unsuitable. Therefore, molecular trends for M. hyopneumoniae have been outlined and a common terminology and classification based on Variable Number Tandem Repeats (VNTR) types has been proposed

The Impact of Dietary Analyzed Calcium to Phosphorus Ratios and Standardized Total Tract Digestible Phosphorus to Net Energy Ratios on Growth Performance, Bone, and Carcass Characteristics of Pigs

A total of 2,184 pigs (PIC 337 × 1050; initially 27.3 lb) were used to evaluate the effects of feeding varying analyzed calcium to phosphorus (Ca:P) ratios at two levels of standardized total tract digestible (STTD) P:NE. Pens of pigs (26 pigs per pen) were assigned to 6 dietary treatments in a randomized complete block design with 14 pens per treatment. Diets consisted of two levels of STTD P:NE, including the PIC recommendation (1.8, 1.62, 1.43, 1.25, 1.10, and 0.99 g STTD P/Mcal NE from 25 to 50, 50 to 90, 90 to 130, 130 to 180, 180 to 230, and 230 to 280 lb, respectively); or 75% of the PIC recommendation, and 3 analyzed Ca:P ratios: 0.90:1, 1.30:1, and 1.75:1. Diets were corn-soybean meal-based and contained phytase (Quantum Blue G, AB Vista, Marlborough, Wiltshire, UK); 500 to 210 FTU/kg with release values from 0.13 to 0.07% STTD P. There was a Ca:P × STTD P:NE interaction (P \u3c 0.05) observed for average daily gain (ADG), feed efficiency (F/G), and final body weight (BW). For ADG and final BW, when feeding 75% of PIC STTD P recommendation, increasing the analyzed Ca:P ratio decreased ADG and final BW (linear, P \u3c 0.001). However, when feeding the PIC STTD P recommendation, increasing the analyzed Ca:P ratio tended to improve ADG and final BW (linear, P \u3c 0.10). For F/G, when feeding 75% of the PIC STTD P recommendation, increasing the analyzed Ca:P ratio tended to worsen F/G (linear, P \u3c 0.10), whereas in pigs fed diets that met PIC STTD P recommendations, increasing the analyzed Ca:P ratio tended to improve F/G in a quadratic (P \u3c 0.10) manner. Despite the interactions, pigs fed the PIC STTD P recommendations had increased ADG, final BW, and improved F/G compared to pigs fed 75% of PIC STTD P recommendations (P \u3c 0.001). In summary, pigs fed at PIC STTD P recommendations had improved overall ADG and F/G compared to pigs fed diets at 75% of PIC STTD P recommendations. Additionally, increasing the analyzed Ca:P ratio worsened ADG and F/G when STTD P was below PIC recommendations but had marginal impacts when adequate STTD P was fed

Effects of Feeding Increasing Standardized Ileal Digestible Lysine on Growth Performance of 26- to 300-lb PIC Line 800-Sired Pigs

The objective of this study was to evaluate the growth performance and economic returns of PIC 800 × 1050 pigs fed increasing SID Lys from approximately 26 to 300 lb. Pens of pigs were blocked by BW and randomly assigned to 1 of 5 dietary treatments in a randomized complete block design with 26 pigs per pen and 16 pens per treatment. Pens were provided 1 of 5 dietary treatments with increasing SID Lys at 85, 93, 100, 107, and 115% of current PIC recommendations within 6 different phases. Two base diets containing low Lys and high Lys were blended to meet target SID Lys levels for each treatment diet within phase. For the overall experimental period (d 0 to 143), feeding increasing SID Lys improved (linear, P ≤ 0.007) ADG and F/G, but did not impact ADFI (P \u3e 0.10). For carcass characteristics, a tendency (linear, P = 0.067) for increased HCW of pigs that were provided increasing SID Lys was observed. However, there was no evidence for differences (P \u3e 0.10) across treatments in carcass yield, backfat depth, loin depth, or carcass lean percentage. Increasing SID Lys of the diets increased (linear, P \u3c 0.001) feed cost and feed cost per lb of gain. There was no evidence of difference (P \u3e 0.10) in revenue for either ingredient price scenario, thus, feeding increasing levels of SID Lys reduced (linear, P \u3c 0.001) income over feed cost (IOFC) in both scenarios. The linear model (LM) served as the best fit for both growth and economic parameters. The LM model predicted maximum ADG and minimal F/G at levels greater than 115% of PIC’s current SID Lys recommendations. For IOFC, the LM model predicted maximum profitability at or below 85% of PIC’s current Lys recommendations. In conclusion, the optimal SID Lys level for PIC 800 × 1050 pigs from 26- to 300-lb depends upon the response criteria, with growth performance maximized at levels at or above 115% of PIC’s recommendation for SID Lys; however, economic responses were maximized at or below 85% of PIC’s current SID Lys recommendations

Effects of Standardized Ileal Digestible Threonine to Lysine Ratio on Growth Performance of PIC Line 337 × 1050 Pigs

The objective of this research was to evaluate the impact of varying SID Thr:Lys ratios on growth performance, removals, and mortality rates of late-nursery, grower, and finishing PIC 337 × 1050 pigs. In each experiment, pens of pigs were blocked by BW and randomly assigned to 1 of 5 dietary treatments in a randomized complete block design with 19 to 27 pigs per pen and 8, 7, and 7 replications per treatment in Exp. 1, 2, and 3, respectively. In Exp. 1, 987 pigs (initially 26.0 ± 0.70 lb) were used from 26 to 54 lb. In Exp. 2, 875 pigs (initially 95.5 ± 1.17 lb) were used from 95 to 155 lb. In Exp. 3, 824 pigs (initially 224.4 ± 1.85 lb) were used from 224 to 297 lb. Pens were randomly assigned to 1 of 5 dietary treatments with increasing SID Thr:Lys ratios at 53, 58, 62, 65, and 68% in Exp. 1 and 2, and 56.5, 60, 64, 68, and 72.5% in Exp. 3. Diets were corn-soybean meal-based. Diets with the lowest and highest Thr:Lys ratios were blended to achieve the target SID Thr:Lys treatments in each experiment. Between experiments, all pens of pigs were placed on a common diet for 23 (Exp. 1 and 2) and 32 d (Exp. 2 and 3) to provide opportunity for compensatory growth prior to initiation of the next experiment. In Exp. 1 (26 to 54 lb), ADG and final BW increased linearly (P ≤ 0.006) while ADFI, Thr intake/d, and Thr intake/kg of gain increased quadratically (P ≤ 0.001). Overall, F/G improved (quadratic, P ≤ 0.001) as Thr:Lys ratio increased. Additionally, Lys intake/d increased (quadratic, P \u3c 0.001) while Lys intake/ kg of gain decreased (quadratic, P\u3c 0.001) with increasing Thr:Lys ratio. The quadratic polynomial (QP) model predicted greater than 68% SID Thr:Lys was required for ADG from 26 to 54 lb, while a QP model suggested that minimum F/G was achieved at 62.1% SID Thr:Lys. In Exp. 2 (95 to 155 lb), ADG, final BW, Thr intake/d, and Thr intake/kg of gain increased (linear, P ≤ 0.05) and F/G improved (linear, P = 0.030) as dietary Thr:Lys increased. Moreover, Lys intake/kg of gain decreased (linear, P = 0.023) with increasing Thr:Lys ratio. For model analysis, QP models suggested optimum ADG and F/G were achieved at levels greater than 68% SID Thr:Lys. However, similar fitting broken-line quadratic (BLQ) and broken-line linear (BLL) models predicted no further improvement to F/G and ADG beyond 61 and 67% SID Thr:Lys, respectively. In Exp. 3 (224 to 297 lb), increasing SID Thr:Lys increased (linear, P ≤ 0.001) Thr intake/d and Thr intake/kg of gain. In addition, increasing SID Thr:Lys ratios tended (P ≤ 0.086) to quadratically increase (P≤ 0.086) ADFI and BW of pigs at the second marketing event. However, no other response criteria were impacted (P ≥ 0.10) by dietary Thr:Lys. Due to a lack of ADG and F/G responses, prediction models were not developed. In summary, these results suggest the optimal SID Thr:Lys level for 26- to 54-lb pigs is 62.1% for feed efficiency and greater than 68% for ADG. From 95 to 155 lb, the requirement was predicted at or above 61 and 67% SID Thr:Lys for F/G and ADG, respectively. However, with the variation in response criteria in Exp. 3 (224 to 297 lb), we were unable to statistically define a requirement estimate

Effects of Standardized Ileal Digestible Tryptophan to Lysine Ratio on Growth Performance of PIC Line 337 × 1050 Pigs

The objective of these experiments was to evaluate the impact of varying SID Trp:Lys ratios on growth performance, removals, and mortality rates of PIC 337 × 1050 finishing pigs. In each experiment, pens of pigs were blocked by BW and randomly assigned to 1 of 5 dietary treatments in a randomized complete block design with 22 to 27 pigs per pen and 6 or 7 replications per treatment. In Exp. 1, 840 pigs (initially 101.2 ± 2.08 lb) were used from 101 to 161 lb. In Exp. 2, 801 pigs (initially 219.8 ± 3.44 lb) were used from 220 to 281 lb. Dietary treatments were corn-soybean meal-based with 30 or 20% DDGS (Exp. 1 and 2, respectively) and contained increasing SID Trp:Lys ratios at 15, 17.5, 19, 21, and 23%. Diets containing low and high Trp:Lys ratios were blended to achieve the target SID Trp:Lys treatment levels in Exp. 1, while diets containing low, medium, and high Trp:Lys ratios were blended to achieve the target SID Trp:Lys treatment levels in Exp. 2. Between experiments, all pens of pigs were placed on a common diet for 27 d and pens were reallotted to dietary treatment at the start of Exp. 2. In Exp. 1, increasing the SID Trp:Lys ratio increased (quadratic, P ≤ 0.008) ADG, ADFI, and final BW and improved (quadratic, P = 0.007) F/G. As expected, increasing SID Trp:Lys increased (linear, P \u3c 0.001) Trp intake, g/d. In addition, Trp intake per kg of gain and Lys intake/d increased (quadratic, P ≤ 0.009), while Lys intake per kg of gain decreased (quadratic, P = 0.008) with increasing SID Trp:Lys ratio. There was no difference between Trp:Lys ratios on the percentage of removals, mortalities, or total removals (P \u3e 0.10). For model analysis in 101- to 161-lb pigs, the developed broken-line linear models suggested no further improvement to ADG and F/G beyond 19.0 and 19.3% SID Trp:Lys, respectively. Meanwhile, a similar fitting quadratic polynomial (QP) model suggested minimum F/G was achieved at 21.5% SID Trp:Lys. In Exp. 2, increasing the SID Trp:Lys ratio increased (linear, P ≤ 0.001) Trp intake and Trp intake per kg of gain (quadratic, P = 0.050). However, no other observed response criteria were significantly impacted (P≥ 0.10). Models to predict optimal Trp:Lys ratios were not analyzed for 220- to 281-lb pigs due to the lack of observed differences for ADG and F/G. In summary, these results suggest the optimal SID Trp:Lys level for 101- to 161-lb pigs was predicted at or above 19.0 and 19.3% SID Trp:Lys for ADG and F/G, respectively. With the variation in response criteria observed in Exp. 2 (220 to 281 lb), we were unable to statistically define a requirement estimate

Diurnally Entrained Anticipatory Behavior in Archaea

By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms). The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature) on O2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime

Genome organization in Halobacterium halobium: a 70 kb island of more (AT) rich DNA in the chromosome.

The more A + T rich fractionated component (FII DNA) of the Halobacterium halobium genome constitutes one third of the total DNA and upon isolation consists of covalently closed circular DNA (pHH1 and minor cccDNA) and nonsupercoiled sequences. We have investigated the physical organization of the non cccDNA in FII by a chromosome walk using one copy of the halobacterial insertion element ISH1 as a start point. This chromosome walk led to the isolation of 160 kb of chromosomal DNA containing 70 kb of FII DNA covalently linked to more G + C rich sequences (FI DNA). Copies of three previously characterized insertion elements (ISH1, ISH2, and ISH26) as well as at least 10 other repeated sequences are clustered within this chromosomal FII DNA "island". Unique sequences are found in the FI DNA flanking the FII DNA island as well as in 40 kb of FI DNA surrounding the bacterio-opsin gene. The presence of pHH1 in H. halobium and closely related species correlates with the occurrence of the characterized chromosomal FII DNA island. Halophilic purple membrane producing isolates YC81819-9, GN101, SB3 and GRA lack pHH1 and the 70 kb FII DNA, but contain all of the FI DNA sequences tested. We propose that pHH1 and this chromosomal FII DNA are characteristic genomic components of H. halobium and closely related species, and, that the 70 kb FII DNA might represent a large insertion in the chromosome of H. halobium and closely related species. The conservation of both FI and FII DNA sequences can be used for strain classification and determination of evolutionary relationships among halo-bacteria