Correction: Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens

[This corrects the article DOI: 10.1371/journal.pone.0301110.].

Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens

The present study was undertaken to profile and compare the cecal microbial communities in conventionally (CONV) grown and raised without antibiotics (RWA) broiler chickens. Three hundred chickens were collected from five CONV and five RWA chicken farms on days 10, 24, and 35 of age. Microbial genomic DNA was extracted from cecal contents, and the V4-V5 hypervariable regions of the 16S rRNA gene were amplified and sequenced. Analysis of 16S rRNA sequence data indicated significant differences in the cecal microbial diversity and composition between CONV and RWA chickens on days 10, 24, and 35 days of age. On days 10 and 24, CONV chickens had higher richness and diversity of the cecal microbiome relative to RWA chickens. However, on day 35, this pattern reversed such that RWA chickens had higher richness and diversity of the cecal microbiome than the CONV groups. On days 10 and 24, the microbiomes of both CONV and RWA chickens were dominated by members of the phylum Firmicutes. On day 35, while Firmicutes remained dominant in the RWA chickens, the microbiome of CONV chickens exhibited am abundance of Bacteroidetes. The cecal microbiome of CONV chickens was enriched with the genus Faecalibacterium, Pseudoflavonifractor, unclassified Clostridium_IV, Bacteroides, Alistipes, and Butyricimonas, whereas the cecal microbiome of RWA chickens was enriched with genus Anaerofilum, Butyricicoccu, Clostridium_XlVb and unclassified Lachnospiraceae. Overall, the cecal microbiome richness, diversity, and composition were greatly influenced by the management program applied in these farms. These findings provide a foundation for further research on tailoring feed formulation or developing a consortium to modify the gut microbiome composition of RWA chickens.

Comparative efficacy of commercially available deoxynivalenol detoxifying feed additives on growth performance, total tract digestibility of components, and physiological responses in nursery pigs fed diets formulated with naturally contaminated corn

Comparative efficacy of deoxynivalenol (DON) detoxifying feed additives (FA) was evaluated in growth performance (exp. 1) and apparent total tract digestibility (ATTD; exp. 2) nursery pig studies. Six corn-soybean meal-based diets were used: 1) positive control (PC, formulated with <1.5 ppm DON corn), negative control (NC, formulated with 5.5 ppm DON corn), NC + FA1 (clay plus yeast cell wall extract), NC + FA2 (aluminosilicate), NC + FA3 (aluminosilicate plus fungal extract), and NC + FA4 (sodium metabisulfite, SMB). In exp. 1, 144 pigs (body weight [BW], 10.2 ± 0.1kg) were housed (4 pigs/pen), allocated to diets (n = 6) based on BW, and fed for 4-wk. The BW and feed intake were monitored weekly. On d 7, one pig/pen was bled for plasma and euthanized for organ weight and tissue samples. Assayed DON concentration in PC, NC, NC + FA4 was 0.29, 2.86, and 1.21 ppm, respectively. In wk-1, the average daily gain (ADG) of pigs fed NC + FA4 was not different (P > 0.05) to that of pigs fed PC diet but greater (P = 0.01) than for pigs fed NC without or with other FA. Pigs fed NC and NC + FA2 had lower (P = 0.026) average daily feed intake (ADFI) than pigs fed PC and NC + FA3. Pigs fed NC + FA4 had greater (P = 0.003) G:F than pigs fed the other diets. Diets had no effect (P > 0.05) on ADG, ADFI, and G: F after first week, plasma concentration of urea and creatinine or liver and spleen weight. Pigs fed NC diets had greater (P = 0.01) jejunal mRNA expression of superoxide dismutase 1 relative to pigs fed PC or NC plus FA. Jejunal histomorphology and mRNA expression of nutrient transporters, inflammatory cytokines, and tight junction proteins and ceca digesta concentration of short-chain fatty acids were not affected (P > 0.05) by the diet. In exp. 2, 24 barrows (BW 10.2 ± 0.3 kg) were individually placed in metabolism crates and allocated to four diets: PC, NC, NC + FA3, and NC + FA4 (n = 6) containing TiO₂ as digestibility marker. Pigs were adjusted to diets for 5 d, followed by a 2-d grab fecal sample collection. Pigs fed PC and NC + FA4 diets had higher ATTD of dry matter, gross energy, and crude protein than NC fed pigs. The FA3 was intermediate in digestibility response. In conclusion, FA containing sequestering component plus fungal extract or SMB in DON-contaminated feed resulted in commensurate nursery pig performance to PC. The tested FA mitigated intestinal oxidative stress through decreased expression of genes for superoxide dismutase.

357 Evaluation of growth performance and physiology of nursery pigs fed deoxynivalenol (DON) contaminated feed supplemented with commercial feed additives (CFA)

Four commercial feed additives (CFA) were evaluated for efficacy in detoxifying deoxynivalenol (DON) in diets fed to 144 nursery pigs (BW 9.80+/- 0.5kg; 2 gilts, and 2 barrows/pen). Six test corn-soybean-meal based diets were: 1) positive control (PC), formulated with clean corn (NC), 2) formulated with contaminated corn (5.5 ppm DON), 3) NC with enzyme+binder1 (NCB1), 4) NC with clay (NCC), 5) NC with enzyme+binder2 (NCB2) and 6) NC with sodium metabisulfite (NCP). Diets were allocated to pens (n = 6) based on BW and fed ad-libitum for 4-wk; BW and feed intake were monitored weekly. At the end of wk-1, one pig/pen was euthanized for tissue collection. Assayed DON concentration for PC, NC, NCB1, NCC, NCB2 and NCP were 0.38, 2.3, 2.3, 2.3, 2.4, and 1.9 ppm, respectively. Diet effects were only observed for ADG and G:F in wk-1; pigs fed NCP had higher (P = 0.01) ADG compared to pigs fed NC and NCC, whilst pigs fed other diets had intermediate and similar ADG (P > 0.05) to pigs fed NC or NCC. Pigs fed NCP showed higher (P = 0.02) G:F relative to pigs fed other diets. The final BW was 31.3, 30.8, 30.4, 30.8, 31.1 and 32.2kg for PC, NC, NCB1, NCC, NCB2 and NCP-fed pigs, respectively. There were no (P > 0.05) diet effects on ADFI throughout the study. There was no (P > 0.05) diet effects on liver and spleen weight, jejunum morphology and concentration of plasma creatinine and urea. Ceca digesta concentration of citric acid was higher (P = 0.03) in pigs fed NCP than pigs fed NCB2. In conclusion, the lack of differences between PC and NC suggested pigs were tolerant to higher DON levels than the regulated dietary maximum of 1 ppm. Improved ADG and G:F due to NCP vs. NC was transient and was not linked to physiological responses.

Identification of stable reference genes for quantitative PCR in koalas

To better understand host and immune response to diseases, gene expression studies require identification of reference genes with stable expression for accurate normalisation. This study describes the identification and testing of reference genes with stable expression profiles in koala lymph node tissues across two genetically distinct koala populations. From the 25 most stable genes identified in transcriptome analysis, 11 genes were selected for verification using reverse transcription quantitative PCR, in addition to the commonly used ACTB and GAPDH genes. The expression data were analysed using stable genes statistical software - geNorm, BestKeeper, NormFinder, the comparative ΔCt method and RefFinder. All 13 genes showed relative stability in expression in koala lymph node tissues, however Tmem97 and Hmg20a were identified as the most stable genes across the two koala populations.

Assessing natural isothiocyanate air emissions after field incorporation of mustard cover crop

A regional air assessment was performed to characterize volatile natural isothiocyanate (NITC) compounds in air during soil incorporation of mustard cover crops in Washington State. Field air sampling and analytical methods were developed specific to three NITCs known to be present in air at appreciable concentrations during/after field incorporation. The maximum observed concentrations in air for the allyl, benzyl, and phenethyl isothiocyanates were respectively 188, 6.1, and 0.7 μg m(-3) during mustard incorporation. Based on limited inhalation toxicity information, airborne NITC concentrations did not appear to pose an acute human inhalation exposure concern to field operators and bystanders.

Comparative evaluation of a bioluminescent bacterial assay in terrestrial ecotoxicity testing

Despite the widespread and successful use of luminescence-based bioassays in water testing, their applications to soils and sediments is less proven. In part this is because such bioassays have mainly been carried out in an aqueous-based medium and, as such, favour contaminants that are readily water-soluble. In this study, aqueous solutions and soils contaminated with heavy metals (HM), polar organic contaminants and hydrophobic organic contaminants (HOCs) were tested using a range of luminescence-based bioassays (Vibrio fischeri, Escherichia coli HB101 pUCD607 and Pseudomonas fluorescens 10586r pUCD607). For the first two chemical groups, the assays were highly reproducible when optimised extraction procedures were employed but for HOCs the bioassay response was poor. Quantitative structure-activity relationships (QSARs) obtained from aqueous solutions had a linear response although correlation for the chemicals tested using bacterial bioassays was significantly less sensitive than that of sublethal tests for Tetrahymena pyriformis. Bacterial and Dendrobaena veneta bioassay responses to extracts from HM amended soils showed that a clear relationship between trophic levels could be obtained. There is no doubt that the wide range of bioluminescent-based bioassays offers complementary applications to traditional testing techniques but there is a significant need to justify and optimise the extraction protocol prior to application.

Letting the family know: balancing ethics and effectiveness when notifying relatives about genetic testing for a familial disorder

OBJECTIVE

To increase the awareness among at risk relatives of the availability of genetic testing for a familial disorder while respecting their autonomy and privacy.

METHODS

This was a comparison of preintervention and postintervention cohorts of families carried out in a state wide clinical service providing genetic counselling and testing for people at risk of familial adult onset cancer. Unaffected relatives who were not clients of the service in 74 kindreds with familial mutations causing familial breast and ovarian cancer, hereditary non-polyposis colorectal cancer, or Cowden syndrome were included in the study. In the baseline cohort (41 kindreds), family members who were clients of the clinical service and had been shown to be carriers of mutations were asked to advise relatives that genetic testing was available. In the intervention cohort (33 kindreds), the clinical service obtained consent to advise at risk relatives by letter that genetic testing was available. The main outcome measures were: (a) proportion of unaffected first and second degree relatives of the proband in each family whose genetic status was clarified within 2 years of the mutation being identified in the family, and (b) concerns regarding privacy and autonomy voiced by relatives receiving these letters.

RESULTS

In the baseline cohort, the average proportion of relatives in each family whose genetic status was clarified was 23%. In the intervention cohort, the average proportion of relatives in each family whose genetic status was clarified was 40% (p = 0.001). None of the relatives in the intervention cohort complained of a breach of privacy or autonomy.

CONCLUSION

Clinical services can take an effective and proactive approach to notifying relatives who are not their clients of the availability of genetic testing without compromising principles of privacy and autonomy.

Naturally occurring spirochetes in the colonic mucosa of raccoons (Procyon lotor)

The large intestines of 21 raccoons (Procyon lotor; 11 wild caught, 10 laboratory confined) were examined for the presence of intestinal spirochetes. Light microscopy of sections stained with hematoxylin and eosin and Warthin-Starry stain showed the presence of spiral shaped organisms deep within the lumina of intestinal glands at the ileocolonic junction of 16 raccoons (76% prevalence). All laboratory-confined, group-housed raccoons harbored the organisms, but only 6/11 (55% prevalence) live-trapped raccoons were positive for these spirochetes. The organisms were free in the glandular lumina, and there were no microscopic lesions. Two types of spirochetes were identified in the colonic glands: a slender spirochete 10-13 microm in length, 0.3 microm in diameter, and possessing long, thin tapered ends and a larger, regularly waved spiral organism (0.5 microm in diameter). The slender spirochete did not resemble any of the known spirochete genera and failed to grow on medium used to propagate oral treponemes and members of the genus Brachyspira.

Penicillin-binding proteins in Leptospira interrogans

The Leptospira interrogans ponA and pbpB genes were isolated and characterized. ponA and pbpB encode the penicillin-binding proteins (PBPs) 1 and 3, respectively. There is little sequence variation between the PBP genes from two L. interrogans strains (serovar icterohaemorrhagiae strain Verdun and serovar pomona strain RZ11). The deduced L. interrogans PBP 1 and PBP 3 protein sequences from the two strains shared over 50% similarity to homologous proteins from Escherichia coli. It was demonstrated for strain Verdun that ponA and pbpB are transcribed individually from their own promoter. The ponA and pbpB genes from both strains are separated by 8 to 10 kb and oriented such that their transcription is convergent. The L. interrogans PBP 1 and PBP 3 proteins were synthesized in E. coli and were modified with ampicillin using a digoxigenin-ampicillin conjugate. These data show that both genes encode functional PBPs.

Expectations and quality of life of cancer patients undergoing radiotherapy

Expectations, real or false, affect the way patients respond to their illnesses. We assessed therapy-related expectations in relation to global quality of life in 55 cancer patients before and after radiotherapy. Factor analysis indicated that therapy-related expectations come into three broad categories--pain/emotional control, healing and tumour/symptom control. 35 patients expected 'healing' even though curative treatment was intended in only 19 and all patients had been fully informed. The expectation of healing was associated with high quality of life, and the same was true of perception of healing after radiotherapy. In the group as a whole, quality of life was little altered by radiotherapy, but it became substantially worse in those patients who had expected healing but perceived that this had failed, even though physician-assessed Karnofsky status did not change. These findings indicate that the expectation of healing, in cancer patients, is a component of a good global quality of life, whereas more limited expectations (pain control, tumour control) relate to lower quality of life. Patients' expectations deserve further study as a novel approach to improving care.

[Radiotherapy in surgical and nonsurgical patients. Therapy expectations, quality of life and physician assessment]

The present study investigates patients' expectations toward radiotherapy and their associations to quality of life and physician judgements. Fifty-five patients with tumors of different sites (30 with previous tumor-related surgery, 25 without surgery) admitted to the department of radiotherapy filled out a standardized questionnaire (EORTC QLQ-C30, PLC by Siegrist et al., therapy-related expectations and success) before and after inpatient radiotherapy. The corresponding physician ratings were collected. Fifty-eight percent of the patients expected the therapeutic goal "healing", whereas from the physician's standpoint this was realistic in only 7% of cases. The specific radiotherapy-related expectations "tumor control" and "pain relief" reached almost the same levels in patients and physician (71% vs 71% and 40% vs 44%). Patients with healing expectancy reported higher quality of life at the beginning of the therapy (53.4% vs 39.9%); patients expecting pain relief reported lower quality of life (37.1% vs 54.5%). Surgical patients who had been operated on within the past year (n = 18) showed a particularly high healing expectancy (83%), whereas patients whose operation dated back more than 1 year focused on pain relief as therapeutic goal (83%). The surgeon, as the primary contact person for patients, can influence patients' therapy-related expectations. In explaining the overall therapeutic strategy, surgeons should also mention the scope and limits of adjuvant therapies.