MilkOligoThesaurus, a dataset of mammalian milk oligosaccharide synonyms

There is a growing interest in milk oligosaccharides (MOs) because of their numerous benefits for newborns' and long-term health. A large number of MO structures have been identified in mammalian milk. Mostly described in human milk, the oligosaccharide richness, although less broad, has also been reported for a wide range of mammalian species. The structure of MOs is particularly difficult to report as it results from the combination of 5 monosaccharides linked by various glycosidic bonds forming structurally diverse and complex matrices of linear and branched oligosaccharides. Exploring the literature and extracting relevant information on MO diversity within or across species appears promising to elucidate structure-function role of MOs. Currently, given the complexity of these molecules, the main issues in exploring literature to extract relevant information on MO diversity within or across species relate to the heterogeneity in the way authors refer to these molecules. Herein, we provide a thesaurus (MilkOligoThesaurus) including the names and synonyms of MOs collected from key selected articles on mammalian milk analyses. MilkOligoThesaurus gathers the names of the MOs with a complete description of their monosaccharide composition and structures. When available, each unique MO molecule is linked to its ID from the NCBI PubChem and ChEBI databases. MilkOligoThesaurus is provided in a tabular format. It gathers 245 unique oligosaccharide structures described by 22 features (columns) including the name of the molecule, its abbreviation, the chemical database IDs if available, the monosaccharide composition, chemical information (molecular formula, monoisotopic mass), synonyms, its formula in condensed form, and in abbreviated condensed form, the abbreviated systematic name, the systematic name, the isomer group, and scientific article sources. MilkOligoThesaurus is also provided in the SKOS (Simple Knowledge Organization System) format. This thesaurus is a valuable resource gathering MO naming variations that are not found elsewhere for (i) Text and Data Mining to enable automatic annotation and rapid extraction of milk oligosaccharide data from scientific papers; (ii) biology researchers aiming to search for or decipher the structure of milk oligosaccharides based on any of their names, abbreviations or monosaccharide compositions and linkages.

Coprophagia in early life tunes expression of immune genes after weaning in rabbit ileum

Coprophagia by suckling rabbits, i.e. ingestion of feces from their mother, reduces mortality after weaning. We hypothesized that this beneficial effect of coprophagia is immune-mediated at the intestinal level. Therefore, this study investigated immune development after weaning by analyzing the ileal transcriptome at day 35 and 49 in rabbits with differential access to coprophagia in early life. Rabbit pups had access between day 1 and 15 to (i) no feces (NF) or (ii) feces from unrelated does (Foreign Feces, FF) or (iii) feces from unrelated does treated with antibiotics (FFab). 350 genes were differentially expressed between day 35 and day 49 in suckling rabbits with access to coprophagia. These genes coded for antimicrobial peptides, a mucin, cytokines and chemokines, pattern recognition receptors, proteins involved in immunoglobulin A secretion and in interferon signaling pathway. Strikingly, prevention of coprophagia or access to feces from antibiotic-treated does in early life blunted immune development between day 35 et 49 in the ileum of rabbits. Thus, coprophagia might be crucial for the maturation of intestinal immunity in rabbits and could explain why this behavior improves survival.

Milk replacer feeding once or twice a day did not change the ruminal metabolomic profile and the microbial diversity of dairy calves from birth to weaning

In commercial dairy production systems, feeding calves once a day could be an alternative to reduce labor expenses. Several studies comparing once (OAD) versus twice (TAD) a day milk feeding systems have not evidenced differences in calf growth, rumen development, blood parameters or health scores, but impact on ruminal microbiota remains to be investigated. The objective of this study was to determine the effects of OAD or TAD on the establishment of the ruminal microbiota and its metabolic activity. Sixteen male calves (45.9 ± 5.7 kg at birth) were involved in the trial from birth to weaning (63 d). After the colostrum phase, 2 feeding programs based on a milk replacer were tested and calves were allocated to these programs on d 5. To study the establishment of the bacterial community, ruminal fluid was obtained from each calf one hour after the morning meal at 7 (d 7), 35 (d 35) and 63 (d 63) days of age. The ruminal metabolome was evaluated at a 7 d interval from d 1 to d 63. Ruminal microbiota and metabolite profiles were characterized by 16 S rRNA gene sequencing- and by H-NMR spectroscopy, respectively. Our results showed that feeding milk replacer once or twice a day did not change the ruminal microbiota and metabolites of dairy calves from birth to weaning. Microbial data showed that diversity and richness increased with age, suggesting a shift from an heterogeneous and less diverse community after birth (d 7) to a more diverse but homogeneous community at 35 and 63 d. These findings suggest that feeding milk once a day can be successfully applied to a calf feeding system without compromising microbial establishment and functions.

Disruption of the primocolonizing microbiota alters epithelial homeostasis and imprints stem cells in the colon of neonatal piglets

The gut microbiota plays a key role in the postnatal development of the intestinal epithelium. However, the bacterial members of the primocolonizing microbiota driving these effects are not fully identified and the mechanisms underlying their long-term influence on epithelial homeostasis remain poorly described. Here, we used a model of newborn piglets treated during the first week of life with the antibiotic colistin in order to deplete specific gram-negative bacteria that are transiently dominant in the neonatal gut microbiota. Colistin depleted Proteobacteria and Fusobacteriota from the neonatal colon microbiota, reduced the bacterial predicted capacity to synthetize lipopolysaccharide (LPS), and increased the concentration of succinate in the colon. The colistin-induced disruption of the primocolonizing microbiota was associated with altered gene expression in the colon epithelium including a reduction of toll-like receptor 4 (TLR4) and lysozyme (LYZ). Our data obtained in porcine colonic organoid cell monolayers suggested that these effects were not driven by the variation of succinate or LPS levels nor by a direct effect of colistin on epithelial cells. The disruption of the primocolonizing microbiota imprinted colon epithelial stem cells since the expression of TLR4 and LYZ remained lower in organoids derived from colistin-treated piglet colonic crypts after several passages when compared to control piglets. Finally, the stable imprinting of LYZ in colon organoids was independent of the H3K4me3 level in its transcription start site. Altogether, our results show that disruption of the primocolonizing gut microbiota alters epithelial innate immunity in the colon and imprints stem cells, which could have long-term consequences for gut health.

The Early Life Microbiota Is Not a Major Factor Underlying the Susceptibility to Postweaning Diarrhea in Piglets

Postweaning diarrhea (PWD) in piglets impair welfare, induce economic losses and lead to overuse of antibiotics. The early life gut microbiota was proposed to contribute to the susceptibility to PWD. The objective of our study was to evaluate in a large cohort of 116 piglets raised in 2 separate farms whether the gut microbiota composition and functions during the suckling period were associated with the later development of PWD. The fecal microbiota and metabolome were analyzed by 16S rRNA gene amplicon sequencing and nuclear magnetic based resonance at postnatal day 13 in male and female piglets. The later development of PWD was recorded for the same animals from weaning (day 21) to day 54. The gut microbiota structure and α-diversity during the suckling period were not associated with the later development of PWD. There was no significant difference in the relative abundances of bacterial taxa in suckling piglets that later developed PWD. The predicted functionality of the gut microbiota and the fecal metabolome signature during the suckling period were not linked to the later development of PWD. Trimethylamine was the bacterial metabolite which fecal concentration during the suckling period was the most strongly associated with the later development of PWD. However, experiments in piglet colon organoids showed that trimethylamine did not disrupt epithelial homeostasis and is thus not likely to predispose to PWD through this mechanism. In conclusion, our data suggest that the early life microbiota is not a major factor underlying the susceptibility to PWD in piglets. IMPORTANCE This study shows that the fecal microbiota composition and metabolic activity are similar in suckling piglets (13 days after birth) that either later develop post-weaning diarrhea (PWD) or not, which is a major threat for animal welfare that also causes important economic losses and antibiotic treatments in pig production. The aim of this work was to study a large cohort of piglets raised in separates environments, which is a major factor influencing the early life microbiota. One of the main findings is that, although the fecal concentration of trimethylamine in suckling piglets was associated with the later development of PWD, this gut microbiota-derived metabolite did not disrupt the epithelial homeostasis in organoids derived from the pig colon. Overall, this study suggests that the gut microbiota during the suckling period is not a major factor underlying the susceptibility of piglets to PWD.

Culture of Piglet Intestinal 3D Organoids from Cryopreserved Epithelial Crypts and Establishment of Cell Monolayers

Intestinal organoids are increasingly being used to study the gut epithelium for digestive disease modeling, or to investigate interactions with drugs, nutrients, metabolites, pathogens, and the microbiota. Methods to culture intestinal organoids are now available for multiple species, including pigs, which is a species of major interest both as a farm animal and as a translational model for humans, for example, to study zoonotic diseases. Here, we give an in-depth description of a procedure used to culture pig intestinal 3D organoids from frozen epithelial crypts. The protocol describes how to cryopreserve epithelial crypts from the pig intestine and the subsequent procedures to culture 3D intestinal organoids. The main advantages of this method are (i) the temporal dissociation of the isolation of crypts from the culture of 3D organoids, (ii) the preparation of large stocks of cryopreserved crypts derived from multiple intestinal segments and from several animals at once, and thus (iii) the reduction in the need to sample fresh tissues from living animals. We also detail a protocol to establish cell monolayers derived from 3D organoids to allow access to the apical side of epithelial cells, which is the site of interactions with nutrients, microbes, or drugs. Overall, the protocols described here is a useful resource for studying the pig intestinal epithelium in veterinary and biomedical research.

The phenotype of the gut region is more stably retained than developmental stage in piglet intestinal organoids

Intestinal organoids are innovative in vitro tools to study the digestive epithelium. The objective of this study was to generate jejunum and colon organoids from suckling and weaned piglets in order to determine the extent to which organoids retain a location-specific and a developmental stage-specific phenotype. Organoids were studied at three time points by gene expression profiling for comparison with the transcriptomic patterns observed in crypts in vivo. In addition, the gut microbiota and the metabolome were analyzed to characterize the luminal environment of epithelial cells at the origin of organoids. The location-specific expression of 60 genes differentially expressed between jejunum and colon crypts from suckling piglets was partially retained (48%) in the derived organoids at all time point. The regional expression of these genes was independent of luminal signals since the major differences in microbiota and metabolome observed in vivo between the jejunum and the colon were not reproduced in vitro. In contrast, the regional expression of other genes was erased in organoids. Moreover, the developmental stage-specific expression of 30 genes differentially expressed between the jejunum crypts of suckling and weaned piglets was not stably retained in the derived organoids. Differentiation of organoids was necessary to observe the regional expression of certain genes while it was not sufficient to reproduce developmental stage-specific expression patterns. In conclusion, piglet intestinal organoids retained a location-specific phenotype while the characteristics of developmental stage were erased in vitro. Reproducing more closely the luminal environment might help to increase the physiological relevance of intestinal organoids.

Effect of live yeast supplementation in sow diet during gestation and lactation on sow and piglet fecal microbiota, health and performance

Feeding probiotics like live yeast Saccharomyces cerevisiae var. boulardii (SB) in pig diets has been suggested to preserve health and reduce antibiotic use during critical periods like weaning. This study was conducted to determine whether SB added in the diet of sows during the last 2 mo of gestation and the 4 wk of lactation may contribute to supporting health and performance of piglets before and after weaning through changes in sow physiology, milk composition and fecal microbiota. Crossbred sows (n=45) from parity 1 to 9 were allocated to two dietary treatments, Control (n=23) and SB (n=22). Sows in the SB group were fed the same standard gestation then lactation diet as the Control sows but with the addition of SB at 1x10 9 colony forming units/kg of feed. Piglets were weaned under challenging conditions consisting in mixing of litters, no pen cleaning and a 2-h period of non-optimal temperature exposure. Blood and feces were collected from sows on d 28 and 113 of gestation and d 6 (feces only) and 28 of lactation, and from piglets on d 6 (feces) and 28 of lactation and d 5 after weaning. Colostrum was collected during parturition and milk on d 6 of lactation. Supplementation of sow diets with SB influenced the fecal microbiota of the sows and their piglets. Five days after weaning, the alpha-diversity was lower (P < 0.05) in piglets from SB sows than in piglets from Control sows. Analysis of microbiota with Partial Least Square Discriminant Analysis discriminated feces from SB sows from that of Control sows at 110 d of gestation (29.4% error rate). Piglet feces could also be discriminated according to the diet of their mother, with a better discrimination early after birth (d 6 of lactation) than after weaning (d 5 post-weaning, 3.4% vs 12.7% error rate). Five d after weaning, piglets had greater white blood cell count, plasma haptoglobin concentration, and oxidative stress than before weaning (P <0.001). Nevertheless, SB supplementation in sow diets had no effect (P > 0.05) on most of health criteria measured in blood and growth performance of piglets during lactation and the post-weaning period. Moreover, dietary supplementation of SB to sows did not elicit any changes (P > 0.05) in their reproductive performance, metabolic and health status, nor in the immunoglobulin and nutrient concentration of colostrum and milk. In the present experimental conditions, feeding SB to sows influenced sow and piglet microbiota with no consequences on their health and performance.

A carvacrol‐based product reduces Campylobacter jejuni load and alters microbiota composition in the caeca of chickens

Aim

This study was conducted to test the ability of a carvacrol‐based formulation (Phodé, France) to decrease the C. jejuni caecal load in inoculated broiler chickens and to study the impact of the C. jejuni inoculation alone or combined with the product, on the caecal microbiota.

Methods and Results

On day 1, chickens were either fed a control feed or the same diet supplemented with a carvacrol‐based product. On day 21, the carvacrol‐supplemented chickens and half of the non‐supplemented chickens were inoculated with C. jejuni (10⁸ CFU). Quantitative PCR was used to quantify C. jejuni in chicken caecal samples and 16S rRNA gene sequencing was carried out at 25, 31 and 35 days of age. A significant decrease of 1.4 log of the C. jejuni caecal load was observed in 35‐day‐old chickens supplemented with the product, compared to the inoculated and unsupplemented group (p < 0.05). The inoculation with C. jejuni significantly increased the population richness, Shannon and Simpson diversity and altered beta‐diversity. Compared to the control group, the C. jejuni inoculation causes significant changes in the microbiota. The carvacrol‐based product associated with C. jejuni inoculation increased the diversity and strongly modified the structure of the microbial community. Functional analysis by 16S rRNA gene‐based predictions further revealed that the product up‐regulated the pathways involved in the antimicrobial synthesis, which could explain its shaping effect on the caecal microbiota.

Conclusions

Our study confirmed the impairment of the caecal bacterial community after inoculation and demonstrated the ability of the product to reduce the C. jejuni load in chickens. Further investigations are needed to better understand the mode of action of this product to promote the installation of a beneficial microbiota to its host.

Significance and Impact of the Study

Results suggested that this product could be promising to control C. jejuni contamination of broilers.

Effect of housing enrichment and type of flooring on the performance and behaviour of female rabbits

This study investigated the effect of housing enrichments (scratching card, gnawing material and a platform), of a change in height and in the type of flooring on the live weight, reproductive performance and behaviour of female rabbits, as well as on the feed intake and spatial distribution of females and their kits. A total of 40 multiparous female rabbits were monitored in three consecutive reproductive cycles (48-d intervals). Four days before parturition in each reproductive cycle, the females were randomly assigned to one of the five types of housing: Control (CNT: 102×47×30 cm, L×W× H); Scratching card (SCT: containing a scratching card); Gnawing materials (GNW: CNT dimensions plus a compressed lucerne hay block and a wooden stick); Platform (PLT: 102×47×60 cm, including a platform with a plastic floor) and Combination (CBN: PLT dimensions with the scratching card, the gnawing materials and a platform). Data were only recorded during the first and third reproductive cycles. The living conditions did not significantly alter the females’ live weight (4889 g at housing; 4890 g at mid-lactation; 4867 g at weaning), reproductive performance (9.0 kits born alive), survival of the kits (90%), nor the feed intake of females and their litters (542 g/day). Providing animals with a gnawing block stimulated Gnawing behaviour (median frequency per group: CTL=0.00, SCT=0.00, GNW=4.69, PLT=0.00, and CBN=2.34; PRearing up behaviour (median frequencies per group: CTL=0.00, SCT=0.00, GNW=0.00, PLT=2.08, and CBN=3.12; P=0.06), and when a platform was present, the rabbits used it (mean values per group: CTL=0.00, SCT=0.00, GNW=0.00, PLT=1.79, and CBN=4.91; P=0.003). Regarding the type of floor, females appeared to prefer the plastic mesh flooring (31.2%) to the wire mesh flooring (18.8%). To sum up, providing female rabbits with simple enrichments appears to stimulate specific behaviours like Gnawing and Rearing up and may contribute to their wellbeing.

Developmental Stage, Solid Food Introduction, and Suckling Cessation Differentially Influence the Comaturation of the Gut Microbiota and Intestinal Epithelium in Rabbits

BACKGROUND

In mammals, the establishment around weaning of a symbiotic relationship between the gut microbiota and its host determines long-term health.

OBJECTIVES

The aim of this study was to identify the factors driving the comaturation of the gut microbiota and intestinal epithelium at the suckling-to-weaning transition. We hypothesized that the developmental stage, solid food ingestion, and suckling cessation contribute to this process.

METHODS

From birth to day 18, Hyplus rabbits were exclusively suckling. From day 18 to day 25, rabbits were 1) exclusively suckling; 2) suckling and ingesting solid food; or 3) exclusively ingesting solid food. The microbiota (16S amplicon sequencing), metabolome (nuclear magnetic resonance), and epithelial gene expression (high-throughput qPCR) were analyzed in the cecum at days 18 and 25.

RESULTS

The microbiota structure and metabolic activity were modified with age when rabbits remained exclusively suckling. The epithelial gene expression of nutrient transporters, proliferation markers, and innate immune factors were also regulated with age (e.g., 1.5-fold decrease of TLR5). Solid food ingestion by suckling rabbits had a major effect on the gut microbiota by increasing its α diversity, remodeling its structure (e.g., 6.3-fold increase of Ruminococcaceae), and metabolic activity (e.g., 4.6-fold increase of butyrate). Solid food introduction also regulated the gene expression of nutrient transporters, differentiation markers, and innate immune factors in the epithelium (e.g., 3-fold increase of nitric oxide synthase). Suckling cessation had no effect on the microbiota, while it regulated the expression of genes involved in epithelial differentiation and immunoglobulin transport (e.g., 2.5-increase of the polymeric immunoglobulin receptor).

CONCLUSIONS

In rabbits, the maturation of the microbiota at the suckling-to-weaning transition is driven by the introduction of solid food and, to a lesser extent, by the developmental stage. In contrast, the maturation of the intestinal epithelium at the suckling-to-weaning transition is under the influence of the developmental stage, solid food introduction, and suckling cessation.

Part-time grouping of rabbit does in enriched housing: effects on performances, injury occurrence and enrichment use

Collective housing is perceived as a possible way to improve rabbit welfare, especially among adult females, which are normally individually housed. Part-time group housing seems to allow a better balance between welfare and health than continuous group housing, but practical implementation and consequences for reproductive performance have not been extensively studied. The aim of this work was to compare weight, feed intake, litter size, injury occurrence, body integrity, and spatial location of female rabbits housed part-time in group housing (PGH group, n = 32) or housed individually (IH group, n = 8). Females were grouped by opening connecting hatches between four individual enriched cages (platform, wood stick and gnawing block). Collective housing started 12 days after artificial insemination and was interrupted at the 10th day (instead of the 15th day later as originally planned) due to high injury rates and severe injuries caused by fighting. The proportion of injured females increased from 25% on the first day of grouping to 63% on the 10th day. Female weight gain during the experiment was similar in the two groups. Litter size at weaning was 9% lower in the PGH group than in the IH group (9.2 vs 10.0, P < 0.01). Platform use was recorded in 32% of the observations and was the highest during the 2 weeks before weaning (46% and 47% of total observations, P < 0.05). During the grouping period, there were at least two females in the same housing unit in 59.4% of the cases, at least two females were located on the same level in 31.3% of the cases. In conclusion, connecting individual cages is an ergonomic solution for part-time group housing, but does not prevent fights for the establishment of a social hierarchy. This is detrimental to the health and body integrity of female rabbits.

Impact of transcatheter aortic valve implantations on temporal trends of pacemaker implantations among French octogenarians: a nation-wide cohort study over the period 2008–2018

Background

The indications for permanent pacemaker implantation (PPMI) are strongly associated with age, with the highest rates for octogenarians (&gt;80 years old). Over the last decade, impact of aging on temporal trends in PPMI rates among octogenarians is questionable. In the 2010's, transcatheter aortic valve implantation (TAVI) has emerged for inoperable or high-risk patients, mainly octogenarians, with an exponential increase over years. PPMI is a common short-term complication after TAVI procedure. Many studies have explored these post-TAVI PPMI in terms of incidence, timing and outcomes of PPMI following TAVI, but there are no data on the impact of TAVI on PPMI temporal trend at a nationwide scale.

Purpose

To evaluate whether PPMI in octogenarians have increased during the last decade, independently from age and sex, on a nationwide scale. Eventually, to estimate the potential contribution of TAVI in PPMI increase in this setting.

Methods

Our study was based on octogenarians from the Echantillon Généraliste de Bénéficiaires, the 1/97 random sample of the French nationwide health insurance claims database. Between 2008 and 2018, we identified de novo PPMI and TAVI with medical procedures codes in the French Common Classification of Medical Procedures (CCAM). Annual incidence rates of PPMI were evaluated between 2008 and 2012 (preTAVI-period). The number of observed PPMI cases, O, in the period 2013–2018 (TAVI-period) was compared with the expected number of PPMI cases, E, calculated by using 2008–2012 incidence rates with age and sex standardization. We then computed the standardized incidence ratio (SIR) of the observed number of PPMI to the expected number of PPMI (O/E), with 95% confidence intervals (CIs). Thereafter, we evaluated the contribution of post-TAVI PPMI in the number of excess cases of PPMI (O-E) for the period 2013–2018.

Results

The population of octogenarians increased from 23,822 in 2008 to 33,752 in 2018. In 2008, 130 PPMI were observed (546/100,000 inhabitants) reaching 228 PPMI (676/100,000) in 2018 with a marked increase in rates from the year 2012. During the period 2013–2018, for all octogenarians, 1242 cases of PPMI were observed, compared with 1171.3 expected cases of PPMI, corresponding to a significant SIR=1.06 (95% CI: 1.01–1.12). For the subpopulation of octogenarians without TAVI, no excess risk was observed with a SIR=1.01 (95% CI: 0.95–1.06). Among the excess cases of PPMI observed in 2013–2018 in all octogenarians, 72% were post-TAVI PPMI.

Conclusion

Based on our study, the number of observed PPMI in octogenarians in period 2013–2018 is 6% higher than the number we would expect. Nearly three-quarter of these excess cases are attributable to TAVI complication.

Funding Acknowledgement

Type of funding sources: None.

Development of a theory-based intervention to increase cognitively able frail elders' engagement with advance care planning using the behaviour change wheel

Background

Advance care planning (ACP) conversations support people to think about, discuss and document their beliefs, values and preferences regarding future care. This process means that should the person loose capacity in the future, care can be provided, consistent with their personal values and beliefs. The ACP process is particularly relevant for older people living with frailty (frail elders) as they are vulnerable to sudden deterioration. However, ACP is rarely undertaken by frail elders. The aim of this study was to develop an intervention to increase multidisciplinary health and social care professionals’ (H&SCPs) engagement of cognitively able, domestic-dwelling frail elders with ACP.

Methods

Intervention development was guided by the Medical Research Council framework for complex interventions and the Behaviour Change Wheel. Multiple methods were used to understand ACP barriers and enablers: a systematic integrative review, a survey (n = 73 H&SCPs), and semi-structured interviews (n = 10 frail elders, n = 8 family members). A conceptual model, developed from the integrative review, underpinned data collection for the survey and interviews. Synthesis of this data, including patient and public involvement, was then used to identify H&SCPs behaviours that needed to change for ACP to be implemented and decide content and implementation for the intervention.

Results

Following the Behaviour Change Wheel system, and based on the findings of the review, survey and interviews, the prototype intervention, Conversations on Living and Dying (CLaD), was developed. The CLaD prototype consisted of one 3.5-hour educational skills session for H&SCPs supported by a toolkit. Content focussed on the relevance of ACP for frail elders, experience of ACP by frail elders, and strategies H&SCPs could adopt to encourage frail elders’ engagement with ACP. Strategies include recognising the importance of relationships and living well now, preparing frail elders for ACP conversations and starting ACP early. Participants who took part in initial prototype refinement reported that the intervention helped them think differently about ACP and encouraged them to engage with frail elders.

Conclusions

The use of behavioural theory enabled the development of CLaD, an evidence-based, theory-driven, person-centred intervention to support ACP engagement with frail elders. While feasibility testing is required, initial prototype refinement demonstrated that H&SCPs found the intervention to be acceptable, engaging, and clinically valuable in their practice with frail elders and their families.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12913-021-06548-4.

495 CONVERSATIONS ON LIVING & DYING: AN INTERVENTION TO INCREASE COGNITIVELY-ABLE, COMMUNITY-BASED FRAIL ELDERS’ ENGAGEMENT WITH ACP

Introduction

Advance care planning (ACP) can support person-centred end-of-life care by helping individuals articulate their end-of-life preferences. Frail elders’ vulnerability to deterioration makes ACP engagement particularly relevant; however, their engagement with ACP is uncommon. This study aimed to develop an intervention to increase ACP engagement with cognitively-able, community-dwelling frail elders.

Methods

Multiple methods were used to establish ACP barriers and facilitators: a systematic integrative review, modified e-Delphi survey (multidisciplinary health and social care professionals (H&SCPs) n = 73), and semi-structured interviews (frail elders n = 10, family members n = 8). A conceptual model, developed from the integrative review, underpinned data collection for the e-Delphi and interviews. Triangulation, including patient and public involvement, was then used to identify H&SCPs behaviours that needed to change and decide intervention content and implementation. The intervention was developed using behavioural change theory. Prototype refinement consisted of pre and post questionnaires, use of the intervention in practice, and focus groups (H&SCPs n = 26).

Results

The prototype intervention consists of a 3.5-hour training and education session for H&SCPs, supported by a toolkit. The intervention focuses on the relevance and experience of ACP for frail elders and ACP strategies H&SCP can use to encourage frail elders’ ACP engagement. Strategies include recognising the importance of decision-making in relationships and living well now, starting early, using an honest but gentle approach, and helping frail elders prepare for ACP conversations. Participants report that the intervention helps them think differently about ACP and encourages them to engage frail elders with ACP.

Conclusions

To our knowledge this is the first intervention underpinned by behaviour theory that focuses on supporting H&SCPs to engage community-dwelling, cognitively-able frail elders with ACP. Refinements, such as additions to the toolkit, have been suggested. However, H&SCPs appear to find the intervention acceptable, feasible, engaging, and useful in their practice.

17 Conversations on Living and Dying: Facilitating Advance Care Planning for Older People Living with Frailty. A Qualitative Study

Introduction

Advance care planning (ACP) is a process that supports people to articulate their future care preferences. This process is a priority for older people living with frailty due to their vulnerability to sudden deterioration, something that has been highlighted during the current pandemic. However, ACP is uncommon for older people living with frailty, hindering choice and person-centred end-of-life care. This study aimed to identify the barriers, facilitators and behaviours required to support cognitively-able, community-dwelling older people living with frailty to engage with ACP. Findings will inform the development an ACP intervention underpinned by behavioural change theory.

Methods

Semi-structured interviews with community-dwelling older people living with frailty (Clinical Frailty Score 6 or 7) and family members were audio-recorded, filmed and transcribed verbatim. A thematic analysis framework was developed using a recent systematic review, and expanded to reflect new themes.

Results

Ten older people living with frailty and eight family members were interviewed. The older people’s median age was 85 and seven were female. Family members were spouses (n = 4) and children (n = 4). The key findings were that: the meaning of ACP could be unclear and at times confusing; many of the older people believed ACP was not relevant to them; relationships and relational autonomy were of greater relevance to older people than autonomous decision-making; older people were more interested in living well now than in planning for the future.

Conclusions

Older people living with frailty need to be engaged with ACP in a way that helps them to understand what ACP is and why it is relevant for them. Professionals need to develop their skills in assessing readiness and facilitating ACP conversations with this population at the older person’s pace. Reframing ACP to include living well now alongside encouraging family inclusion would also relate better to this populations’ lives.

The intestinal microbial composition in Greylag geese differs with steatosis induction mode: spontaneous or induced by overfeeding

Background

Relationships between microbial composition and steatosis are being extensively studied in mammals, and causal relations have been evidenced. In migratory birds the liver can transiently store lipids during pre-migratory and migratory phases, but little is known about the implications of the digestive microbiota in those mechanisms. The Landaise greylag goose (Anser anser) is a good model to study steatosis in migratory birds as it is domesticated, but is still, from a genetic point of view, close to its wild migratory ancestor. It also has a great ingestion capacity and a good predisposition for hepatic steatosis, whether spontaneous or induced by conventional overfeeding. The conventional (overfeeding) and alternative (spontaneous steatosis induction) systems differ considerably in duration and feed intake level and previous studies have shown that aptitudes to spontaneous steatosis are very variable. The present study thus aimed to address two issues: (i) evaluate whether microbial composition differs with steatosis-inducing mode; (ii) elucidate whether a digestive microbial signature could be associated with variable aptitudes to spontaneous liver steatosis.

Results

Performances, biochemical composition of the livers and microbiota differed considerably in response to steatosis stimulation. We namely identified the genus Romboutsia to be overrepresented in birds developing a spontaneous steatosis in comparison to those submitted to conventional overfeeding while the genera Ralstonia, Variovorax and Sphingomonas were underrepresented only in birds that did not develop a spontaneous steatosis compared to conventionally overfed ones, birds developing a spontaneous steatosis having intermediate values. Secondly, no overall differences in microbial composition were evidenced in association with variable aptitudes to spontaneous steatosis, although one OTU, belonging to the Lactobacillus genus, was overrepresented in birds having developed a spontaneous steatosis compared to those that had not.

Conclusions

Our study is the first to evaluate the intestinal microbial composition in association with steatosis, whether spontaneous or induced by overfeeding, in geese. Steatosis induction modes were associated with distinct digestive microbial compositions. However, unlike what can be observed in mammals, no clear microbial signature associated with spontaneous steatosis level was identified.

Gut Microbiota-Derived Metabolite Signature in Suckling and Weaned Piglets

The gut microbiota plays a key role in intestinal development at the suckling-to-weaning transition. The objective of this study was to analyze the production of metabolites by the gut microbiota in suckling and weaned piglets. We studied piglets raised in two separate maternity farms and weaned at postnatal day 21 in the same farm. The fecal metabolome (¹H nuclear magnetic resonance) and the microbiota composition (16S rRNA gene amplicon sequencing) and its predicted functions (PICRUSt2) were analyzed in the same piglets during the suckling period (postnatal day 13) and 2 days after weaning (postnatal day 23). The relative concentrations of the bacterial metabolites methylamine, dimethylamine, cadaverine, tyramine, putrescine, 5-aminovalerate, succinate, and 3-(4-hydroxyphenylpropionate) were higher during the suckling period than after weaning. In contrast, the relative concentrations of the short-chain fatty acids acetate and propionate were higher after weaning than during the suckling period. The maternity of origin of piglets also influenced the level of some bacterial metabolites (propionate and isobutyrate). The fecal metabolome signatures observed in suckling and weaned piglets were associated with specific microbiota-predicted functionalities, structure, and diversity. Gut microbiota-derived metabolites, which are differentially abundant between suckling and weaned piglets (e.g., short-chain fatty acids and biogenic amines), are known to regulate gut health. Thus, identification of metabolome signatures in suckling and weaned piglets paves the way for the development of health-promoting nutritional strategies, targeting the production of bacterial metabolites in early life.

Culture of rabbit caecum organoids by reconstituting the intestinal stem cell niche in vitro with pharmacological inhibitors or L-WRN conditioned medium

Intestinal organoids are self-organized 3-dimensional (3D) structures formed by a single layer of polarized epithelial cells. This innovative in vitro model is highly relevant to study physiology of the intestinal epithelium and its role in nutrition and barrier function. However, this model has never been developed in rabbits, while it would have potential applications for biomedical and veterinary research. Here, we cultured rabbit caecum organoids with either pharmacological inhibitors (2Ki medium) or L-WRN cells conditioned medium (L-WRN CM) to reconstitute the intestinal stem cell niche in vitro. Large spherical organoids were obtained with the 2Ki medium and this morphology was associated with a high level of proliferation and stem cells markers gene expression. In contrast, organoids cultured with L-WRN CM had a smaller diameter; a greater cell height and part of them were not spherical. When the L-WRN CM was used at low concentration (5%) for two days, the gene expression of stem cells and proliferation markers were very low, while absorptive and secretory cells markers and antimicrobial peptides were elevated. Epithelial cells within organoids were polarized in 3D cultures with 2Ki medium or L-WRN CM (apical side towards the lumen). We cultured dissociated organoid cells in 2D monolayers, which allowed accessibility to the apical compartment. Under these conditions, actin stress fibers were observed with the 2Ki medium, while perijonctionnal localization of actin was observed with the L-WRN CM suggesting, in 2D cultures as well, a higher differentiation level in the presence of L-WRN CM. In conclusion, rabbit caecum organoids cultured with the 2Ki medium were more proliferative and less differentiated than organoids cultured with L-WRN CM. We propose that organoids cultured with the 2Ki medium could be used to rapidly generate in vitro a large number of rabbit intestinal epithelial stem cells while organoids cultured with the L-WRN CM used at low concentration represent a suitable model to study differentiated rabbit epithelium.

Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition

In suckling mammals, the onset of solid food ingestion is coincident with the maturation of the gut barrier. This ontogenic process is driven by the colonization of the intestine by the microbiota. However, the mechanisms underlying the microbial regulation of the intestinal development in early life are not fully understood. Here, we studied the co-maturation of the microbiota (composition and metabolic activity) and of the gut barrier at the suckling-to-weaning transition by using a combination of experiments in vivo (suckling rabbit model), ex vivo (Ussing chambers) and in vitro (epithelial cell lines and organoids). The microbiota composition, its metabolic activity, para-cellular epithelial permeability and the gene expression of key components of the gut barrier shifted sharply at the onset of solid food ingestion in vivo, despite milk was still predominant in the diet at that time. We found that cecal content sterile supernatant (i.e. containing a mixture of metabolites) obtained after the onset of solid food ingestion accelerated the formation of the epithelial barrier in Caco-2 cells in vitro and our results suggested that these effects were driven by the bacterial metabolite butyrate. Moreover, the treatment of organoids with cecal content sterile supernatant partially replicated in vitro the effects of solid food ingestion on the epithelial barrier in vivo. Altogether, our results show that the metabolites produced by the microbiota at the onset of solid food ingestion contribute to the maturation of the gut barrier at the suckling-to-weaning transition. Targeting the gut microbiota metabolic activity during this key developmental window might therefore be a promising strategy to promote intestinal homeostasis.

Early Introduction of Solid Feeds: Ingestion Level Matters More Than Prebiotic Supplementation for Shaping Gut Microbiota

Early introduction of a nutritional substrate is a promising biomimetic strategy for controlling the implantation of the microbiota and preserving the health of young animals. In this study, we provided experimental solid substrate in a gel form to stimulate suckling rabbits' intake and to investigate its effects on microbiota implantation and colonization. All the rabbits had access to solid feed outside the nest as of 15 days of age. Except for the control group, rabbits were offered starter feed gels inside the nests from 3 to 18 days of age. These gels were either free of additives (AF_GEL) or contained 4% of fructo-oligosaccharides (FOS_GEL) or 4% of mannan-oligosaccharides and β-glucans mixtures (MOS_GEL). The cecal content of 160 rabbits was sampled at 18, 29, 38, and 57 days of age and analyzed using 16S rRNA gene sequencing. Pups consumed an average of 3.95 ± 1.07 g of starter feed gel with a higher intake when it was supplemented with fructo-oligosaccharides (+1.2 g; P < 0.05). Starter feed gel consumption increased the ensuing intake of pellets (+17 g from 15 to 21 days; P < 0.05). Alpha-diversity indexes were similar between groups and prebiotic supplementation did not induce a clear shift in microbiota pattern. Conversely, when considering rabbits that consumed more starter feed, the highest proportions of bacteria with plant-degrading abilities, such as species from the Lachnospiraceae and Ruminococcaceae families, were observed at 18 days of age. However, fermentative activities were not affected by starter feed intake at 29, 38, and 57 days of age. By providing comprehensive results on the regulation of microbial community structure at the onset of solid feed intake, this research paves the way for further studies on digestive ecosystem maturation.

1H-NMR metabolomics response to a realistic diet contamination with the mycotoxin deoxynivalenol: Effect of probiotics supplementation

Low-level contamination of food and feed by deoxynivalenol (DON) is unavoidable. We investigated the effects of subclinical treatment with DON, and supplementation with probiotic yeast Saccharomyces cerevisiae boulardii I1079 as a preventive strategy in piglets. Thirty-six animals were randomly assigned to either a control diet, a diet contaminated with DON (3 mg/kg), a diet supplemented with yeast (4 × 10⁹ CFU/kg), or a DON-contaminated diet supplemented with yeast, for four weeks. Plasma and tissue samples were collected for biochemical analysis,¹H-NMR untargeted metabolomics, and histology. DON induced no significant modifications in biochemical parameters. However, lesion scores were higher and metabolomics highlighted alterations of amino acid and 2-oxocarboxylic acid metabolism. Administering yeast affected aminoacyl-tRNA synthesis and amino acid and glycerophospholipid metabolism. Yeast supplementation of piglets exposed to DON prevented histological alterations, and partial least square discriminant analysis emphasised similarity between the metabolic profiles of their plasma and that of the control group. The effect on liver metabolome remained marginal, indicating that the toxicity of the mycotoxin was not eliminated. These findings show that the ¹H-NMR metabolomics profile is a reliable biomarker to assess subclinical exposure to DON, and that supplementation with S. cerevisiae boulardii increases the resilience of piglets to this mycotoxin.

Data set on early feed intake and growth performances of rabbits fed during the suckling period with pellets differing in diameter or compression rate using a double-choice testing design

Weaning is a critical period for the health of rabbits, with a high sensitivity to digestive diseases. Allowing early consumption of solid feed in the nest of the suckling rabbit could help to maintain its health around weaning. In general, previous studies have focused on feed intake of rabbits when they are able to leave the nest, i.e. around 16 days. Herein, we provide a unique dataset of the dynamics of the onset of feed intake in suckling rabbits from 8 days to weaning. We quantified the solid feed intake behaviour and determined the dietary preferences for pellets according to their physical properties using nine pellets differing in diameter or compression rate. Additionally to the data provided in Paës et al. [1] we provide (i) the description of the nine pellets processing (ii) the description of the 3 point-scale system for nest quality evaluation, (iii) details on the device used to provide pellets in the nest, (iv) milk intake data and milk intake curve calculation and (v) pellet intake data according to physical characteristics.

Insights into suckling rabbit feeding behaviour: acceptability of different creep feed presentations and attractiveness for sensory feed additives

In young rabbit, digestive disorders are frequently observed around weaning. Stimulating the onset of feed intake in the suckling rabbit might be a way to promote gut health. The aim of this study was to determine the rabbit's acceptability for different feed presentations and its preferences for flavours at an early stage of life. Two trials were conducted to evaluate the effects of physical form and flavouring on creep feed attractiveness. All the diets tested were provided in the nest from 3 to 17 days, and the daily intake per litter was recorded as of 8 days of age. In the first trial, five feed presentations were tested separately (n = 60 litters). Three dry presentations were chosen: commercial pellet (P), crumb from commercial pellet (cP) and crumb from beet pulp pellet (cBP). Hydrated feeds were also provided with either raw fodder beetroot (B) or a semi-solid feed in agar gel form produced with fodder beetroot juice and pulp (gB). In the second trial, double-choice tests were performed on four feed gels (n = 72 litters), leading to six comparison treatments. These agar gels were made of pellet mash without or with a sensory additive: one non-odorised control gel and three gels with 0.20% banana flavour, 0.06% red berry flavour and 0.10% vanilla flavour, respectively. In the first trial, kits ate more gB in fresh matter than other feed presentations (P < 0.001), with a total intake of 7.0 ± 1.8 g/rabbit from 8 to 17 days. In DM, the total consumption of pellets P (1.6 ± 0.4 g of DM/rabbit) was the highest together with the gB form (1.4 ± 0.4 g of DM/rabbit), whereas cBP was barely consumed (0.3 ± 0.1 g of DM/rabbit). Gel feed supplemented with vanilla was slightly more consumed than other flavoured and non-odorised gels (relative consumption of 57% when compared to control gel; P = 0.001). The gel feed intake was independent of the milk intake but was correlated with the litter weight at 3 days (r = 0.40, P < 0.001). In both trials, rabbit growth before and after weaning was not affected by the type of creep feed provided. Our results confirmed that providing creep feed promotes the solid intake of rabbits at early stages. Gel feed form motivated rabbits to eat and vanilla flavour supplementation increased the feed palatability. Those creep feed characteristics should be explored further for seeking effective stimulation of the onset of the feed intake in suckling rabbit.

Empowering minor migrants: peer support program Nantes

Background

Under-aged migrants (UAMs) may see their legal minority unrecognised by the French state. If they confront this decision at court, they stand in a legal void. They can benefit from a direct access to State Medical Aid and are not submitted to a minimum period of 3 months of staying in France unlike adults. Moreover, when accessing care, unrecognised UAMs are in an unclear situation as they are minors without legal representation. This research is based on a newly created program ran by Doctors of the World (MDM) in Nantes, aiming to enhance UAMs access to health care and rights through peer-support. Peer-support is intended to develop the empowerment the UAM and help them to be able to be the authors of their life thus develop their own abilities (Le Grand, 2018). The role of empowerment in health access is established (Wallerstein, 2006). The research aims at identifying the obstacles and levers in the implementation of the program, the modifications it can cause in the program.

Methods

The research is based on 3 months ethnographical observations, 9 formal interviews with UAM, 5 with professionals, and informal interviews.

Results

We identify that volunteers share a different perception of what is empowerment. Some would leave quite a large autonomy to UAMs while others find it difficult to alter the organisation to give space to UAMs. Finally, self-help mainly develops abilities of those UAMs who were more resourceful.

Conclusions

The analysis shows that a successful program of empowerment rely on shared views of its meaning. Moreover it shows that empowerment may help mainly those resourceful thus exacerbate some inequalities in ressources.

Key messages

The notions of empowerment and peer-support need to be well understood by all. Empowerment, as a side effect first exacerbates some inequalities of resources among UAMs.

Intergenerational Transmission of Characters Through Genetics, Epigenetics, Microbiota, and Learning in Livestock

Evolutionary biologists studying wild species have demonstrated that genetic and non-genetic sources of information are inherited across generations and are therefore responsible for phenotypic resemblance between relatives. Although it has been postulated that non-genetic sources of inheritance are important in natural selection, they are not taken into account for livestock selection that is based on genetic inheritance only. According to the natural selection theory, the contribution of non-genetic inheritance may be significant for the transmission of characters. If this theory is confirmed in livestock, not considering non-genetic means of transmission in selection schemes might prevent achieving maximum progress in the livestock populations being selected. The present discussion paper reviews the different mechanisms of genetic and non-genetic inheritance reported in the literature as occurring in livestock species. Non-genetic sources of inheritance comprise information transmitted via physical means, such as epigenetic and microbiota inheritance, and those transmitted via learning mechanisms: behavioral, cultural and ecological inheritance. In the first part of this paper we review the evidence that suggests that both genetic and non-genetic information contribute to inheritance in livestock (i.e. transmitted from one generation to the next and causing phenotypic differences between individuals) and discuss how the environment may influence non-genetic inherited factors. Then, in a second step, we consider methods for favoring the transmission of non-genetic inherited factors by estimating and selecting animals on their extended transmissible value and/or introducing favorable non-genetic factors via the animals’ environment.

Dehydrated Alfalfa and Fresh Grass Supply in Young Rabbits: Effect on Performance and Caecal Microbiota Biodiversity

Simple Summary

The weaning of young rabbits is a critical period that is often accompanied by digestive troubles. Innovations in feeding strategy are urgently needed to preserve rabbit health and to reduce the use of antibiotics. We show here that providing dehydrated alfalfa during weaning is a promising solution to manage health status by favoring the establishment of a proper digestive microbiota.

Abstract

The improvement of rabbit gut microbiota by modifying nutritional components of the feed or favoring its early intake of feed has been previously investigated. The early administration of dehydrated alfalfa (A) or fresh grass (G) for rabbits, during the peri-weaning period (30 and 45 days of age), and their effect on performance and caecal microbiota compared to a standard diet (C) were evaluated. Until 15 days of age, nine litters/group were housed in the maternal cage and milked once per day. From 15 to 30 days, the young rabbits could consume both milk and solid feed (pelleted for C or supplemental feed for A and G). At 30 days of age, the rabbits were weaned and, until 45 days, were kept in single cages following the same dietary protocol. No significant changes were found in the milk intake or the individual weight of young rabbits at 30 and 45 days. The caecal Firmicutes/Bacteroidetes (bacterial phyla ratio) increased with age (from 2.43 to 6.05 on average, at 30 and 45 days). The Ruminococcaceae/Lachinospiraceae (bacterial family ratio) was highest in the A group at both ages, followed by G then C. The early administration of dehydrated alfalfa is a promising solution to improve health status by favoring an appropriate digestive microbiota.

Diversity and Co-occurrence Pattern Analysis of Cecal Microbiota Establishment at the Onset of Solid Feeding in Young Rabbits

This study aimed to evaluate how the feeding strategy of rabbit kits at the onset of solid feed intake could affect ecological diversity and co-occurrence patterns of the cecal bacterial community. From birth to 18 days of age kits were exclusively milk-fed, and between 18 and 35 days the young rabbits also had access to solid feed. After weaning at (35 days), young rabbits were exclusively fed solid feed. Three experimental feeds were used: a high concentrate diet [H: 10.16 MJ digestible energy (DE)/kg and 15.3% crude protein (CP)], a low concentrate diet (L: 9.33 MJ DE/kg and 14.7% CP) and a reproductive female diet (R: 10.57 MJ DE/kg and 17.3% CP). The rabbit kits (n = 357) were divided into three groups, differing by the diet received during two periods: from 18 to 28 and from 28 to 49 days of age. In the groups LL and HH, rabbit kits were fed L or H diets, respectively, during both periods. Kits in the group RL received feeds R and L from 18 to 28 and 28 to 49 days of age, respectively. Cecal bacterial communities of 10 rabbits per group were carried out at 18, 28, 35, 43 and 49 days of age by MiSeq Illumina sequencing 16S rRNA encoding genes. Between 18 and 28 days of age, solid feed intake was higher in the group RL compared to the other two groups (+24%; P < 0.01). Overall, 13.4% of the OTUs detected were present in the cecal ecosystem from 18 to 49 days old, whereas 17.4% were acquired with the onset of solid feeding and kept from 28 days on. Exclusive milk consumption constrains the bacterial community toward a similar structure but high phylogenetic beta-diversity. Introduction of solid feed induced a sharp change of microbial community structure and decreased phylogenetic diversity. A strong relationship in bacterial community network occurred only from 43 days on. Our feeding strategy at the onset of solid feed ingestion exhibited only a moderate effect on the microbial community structure (P = 0.072), although the LL group seemed to reach faster maturity compared to the two other groups.

The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups

Progress in genome sequencing and bioinformatics opens up new possibilities, including that of correlating genome annotations with functional information such as metabolic pathways. Thanks to the development of functional annotation databases, scientists are able to link genome annotations with functional annotations. We present MetAboliC pAthways DAtabase for Microbial taxonomic groups (MACADAM) here, a user-friendly database that makes it possible to find presence/absence/completeness statistics for metabolic pathways at a given microbial taxonomic position. For each prokaryotic 'RefSeq complete genome', MACADAM builds a pathway genome database (PGDB) using Pathway Tools software based on MetaCyc data that includes metabolic pathways as well as associated metabolites, reactions and enzymes. To ensure the highest quality of the genome functional annotation data, MACADAM also contains MicroCyc, a manually curated collection of PGDBs; Functional Annotation of Prokaryotic Taxa (FAPROTAX), a manually curated functional annotation database; and the IJSEM phenotypic database. The MACADAM database contains 13 509 PGDBs (13 195 bacterial and 314 archaeal), 1260 unique metabolic pathways, completed with 82 functional annotations from FAPROTAX and 16 from the IJSEM phenotypic database. MACADAM contains a total of 7921 metabolites, 592 enzymatic reactions, 2134 EC numbers and 7440 enzymes. MACADAM can be queried at any rank of the NCBI taxonomy (from phyla to species). It provides the possibility to explore functional information completed with metabolites, enzymes, enzymatic reactions and EC numbers. MACADAM returns a tabulated file containing a list of pathways with two scores (pathway score and pathway frequency score) that are present in the queried taxa. The file also contains the names of the organisms in which the pathways are found and the metabolic hierarchy associated with the pathways. Finally, MACADAM can be downloaded as a single file and queried with SQLite or python command lines or explored through a web interface.

The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups

Progress in genome sequencing and bioinformatics opens up new possibilities, including that of correlating genome annotations with functional information such as metabolic pathways. Thanks to the development of functional annotation databases, scientists are able to link genome annotations with functional annotations. We present MetAboliC pAthways DAtabase for Microbial taxonomic groups (MACADAM) here, a user-friendly database that makes it possible to find presence/absence/completeness statistics for metabolic pathways at a given microbial taxonomic position. For each prokaryotic 'RefSeq complete genome', MACADAM builds a pathway genome database (PGDB) using Pathway Tools software based on MetaCyc data that includes metabolic pathways as well as associated metabolites, reactions and enzymes. To ensure the highest quality of the genome functional annotation data, MACADAM also contains MicroCyc, a manually curated collection of PGDBs; Functional Annotation of Prokaryotic Taxa (FAPROTAX), a manually curated functional annotation database; and the IJSEM phenotypic database. The MACADAM database contains 13 509 PGDBs (13 195 bacterial and 314 archaeal), 1260 unique metabolic pathways, completed with 82 functional annotations from FAPROTAX and 16 from the IJSEM phenotypic database. MACADAM contains a total of 7921 metabolites, 592 enzymatic reactions, 2134 EC numbers and 7440 enzymes. MACADAM can be queried at any rank of the NCBI taxonomy (from phyla to species). It provides the possibility to explore functional information completed with metabolites, enzymes, enzymatic reactions and EC numbers. MACADAM returns a tabulated file containing a list of pathways with two scores (pathway score and pathway frequency score) that are present in the queried taxa. The file also contains the names of the organisms in which the pathways are found and the metabolic hierarchy associated with the pathways. Finally, MACADAM can be downloaded as a single file and queried with SQLite or python command lines or explored through a web interface.

Saccharomyces cerevisiae Boulardii Reduces the Deoxynivalenol-Induced Alteration of the Intestinal Transcriptome

Type B trichothecene mycotoxin deoxynivalenol (DON) is one of the most frequently occurring food contaminants. By inducing trans-activation of a number of pro-inflammatory cytokines and increasing the stability of their mRNA, trichothecene can impair intestinal health. Several yeast products, especially Saccharomyces cerevisiae, have the potential for improving the enteric health of piglets, but little is known about the mechanisms by which the administration of yeast counteracts the DON-induced intestinal alterations. Using a pig jejunum explant model, a whole-transcriptome analysis was performed to decipher the early response of the small intestine to the deleterious effects of DON after administration of S. cerevisiae boulardii strain CNCM I-1079. Compared to the control condition, no differentially expressed gene (DE) was observed after treatment by yeast only. By contrast, 3619 probes-corresponding to 2771 genes-were differentially expressed following exposure to DON, and 32 signaling pathways were identified from the IPA software functional analysis of the set of DE genes. When the intestinal explants were treated with S. cerevisiae boulardii prior to DON exposure, the number of DE genes decreased by half (1718 probes corresponding to 1384 genes). Prototypical inflammation signaling pathways triggered by DON, including NF-κB and p38 MAPK, were reversed, although the yeast demonstrated limited efficacy toward some other pathways. S. cerevisiae boulardii also restored the lipid metabolism signaling pathway, and reversed the down-regulation of the antioxidant action of vitamin C signaling pathway. The latter effect could reduce the burden of DON-induced oxidative stress. Altogether, the results show that S. cerevisiae boulardii reduces the DON-induced alteration of intestinal transcriptome, and point to new mechanisms for the healing of tissue injury by yeast.

An LPS based method to stimulate the inflammatory response in growing rabbits

<p>Reliable indicators are needed to study the relationship between the inflammatory response of the growing rabbit and breeding factors such as feeding practices. A lipopolysaccharide (LPS) stimulation of the inflammatory response is a valid model of bacterial infection in laboratory animals, but no data on the growing rabbit has yet been obtained. The aim of our study was to determine an adequate dose of LPS to inject in growing rabbits in order to elicit a measurable inflammatory response in terms of plasmatic TNF-α and rise in rectal temperature. Three trials were carried out in this study: 2 development trials, the first (n=18) testing 3 doses of LPS (2, 10, 50 μg/kg) on the plasmatic TNF-α concentration at 90 and 180 min post injection, and the second trial (n=36) testing 4 doses of LPS (50, 75, 100 and 150 μg/kg) on the TNF-α concentration 90 min post injection and the rectal temperature. The third trial was designed as an application of the method in a large number of animals (n=32) to study the effect of feed restriction and dietary increase in digestible fibre to starch ratio on the LPS inflammatory challenge response of growing rabbits. In development trials 1 and 2, animals had measurable TNF-α responses for doses higher than 10 μg/kg at 90 min post injection, with an increase in the number of responsive animals along with the dose. High variability was observed in TNF-α concentrations in responsive animals (coefficient of variation from 44 to 94%). Animals demonstrated an increase in rectal temperature for all doses injected in the range of 50-150 μg/kg from 90 min post injection with a peak at 180 min (Δ_Tr=1.9±0.7°C). Our observations led us to choose a dose of 100 μg/kg of LPS for our following studies, as the responses in terms of temperature and TNF-α were the most satisfactory. The application of our LPS injection protocol to our nutritional study enabled us to validate our protocol (Δ_Tr=1.1±0.7°C at 180 min and 15/32 TNF-α responsive animals) even though we were not able to demonstrate any effect of the feeding level or diet on the inflammatory response to an LPS injection.</p><p> </p>