Canaries' Microbiota: The Gut Bacterial Communities along One Female Reproductive Cycle

Investigations of bacterial communities are on the rise both in human and veterinary medicine. Their role in health maintenance and pathogenic mechanisms is in the limelight of infectious, metabolic, and cancer research. Among the most considered, gut bacterial communities take the cake. Their part in animals was assessed mainly to improve animal production, public health, and pet management. In this regard, canaries deserve attention, being a popular pet and source of economic income for bird-keepers, for whom breeding represents a pivotal point. Thus, the present work aimed to follow gut bacterial communities' evolution along on whole reproductive cycle of 12 healthy female canaries. Feces were collected during parental care, molting, and resting phase, and submitted for 16S rRNA sequencing. Data were analyzed and a substantial presence of Lactobacillus aviarius along all the phases, and a relevant shift of microbiota during molting and rest due to an abrupt decrease of the Vermiphilaceae family were detected. Although the meaning of such change is not clear, future research may highlight unforeseen scenarios. Moreover, Lactobacillus aviarius may be deemed for normal bacteria flora restoration in debilitated birds, perhaps improving their health and productivity.

Immune Response and Fatty Acid Profile of Eggs from Laying Hens Fed Fermented Feed Rich in Polyunsaturated Fatty Acids

Western diets are dominated by the consumption of chemically modified foods, characterized by a deficiency of n-3 polyunsaturated fatty acids (PUFAs). Lack of n-3 PUFAs is also present in livestock feed, which negatively affects livestock health, including immune response, and results in a low content of n-3 PUFAs in animal products. The goal of this experiment was to study the effect of the addition of feed containing PUFAs produced by the fungus Mortierella alpina on immune parameters (IgA, MUC-2, IGF-2, phagocytoses and selected lymphocyte subsets) and the composition of the intestinal microbiota of hens and egg fatty acids profile. Hens were divided into groups (control, F10—supplemented with 10% of fermented feed, F15—supplemented with 15% of fermented feed). The relative expression of all genes was markedly upregulated, mainly in the F15 group. Likewise, in F15, a significant increase in both phagocytes engulfing capacity and the level of oxidative burst was observed. Neither CD T cell subpopulations nor the CD4/CD8 ratio were significantly affected. A significant increase in small intestinal enterobacteria was observed in the F15. The fatty acid profile of eggs in both experimental groups showed an increased proportion of n-3 PUFAs and decreased n-6/n-3 PUFAs ratio. The results of this work show that the addition of 15% omega-3 acids enriched fermented feed positively affected the immune response of laying hens and improved the fatty acid composition of eggs.

Influence of Feeding Omega-3 Polyunsaturated Fatty Acids to Broiler Breeders on Indices of Immunocompetence, Gastrointestinal, and Skeletal Development in Broiler Chickens

Modern broiler chickens are associated with rapid growth rates and superior feed efficiency. However, they are also susceptible to physiological and metabolic disorders (e.g., skin lesions, lameness, sudden death, enteric diseases, myopathies) that exert substantial economic losses to producers. This is further exacerbated by consumer pressure and mandated cessation of production practices such as indiscriminate use of antimicrobial growth promoters. Manipulation of broiler breeder (BB) nutrition and management can influence chick quality, robustness, and resilience to stressors in the production environment. The present review examines the role of feeding BB functional polyunsaturated omega-3 fatty acids (n-3 PUFA) and subsequent impact on the indices of immunocompetence, skeletal, and gastrointestinal (GIT) development in broiler chickens. Research in mammalian and avian models led evidence that perinatal feeding of long chain n-3 PUFA such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) engender transgenerational effects through regulation of a variety of biological processes including development of vital organs such as skeleton, brain and GIT. It is shown that feeding poultry breeders n-3 PUFA decreases inflammatory states and enriches hatching eggs with n-3 PUFA and immunoglobulins. Further evidence also shows that after 15 days of incubation, chicken embryos preferentially utilize long chain n-3 PUFA-critical for optimal cell, tissues, and organ development. Enrichment of n-3 PUFA in newly hatchling tissues reduce proinflammatory eicosanoids with consequences of enhanced bone mineralization. Dietary n-3 PUFA also modulates breeder GIT microbiota with consequences of microbial colonization and succession in chicks. As well, research shows that feeding poultry breeders n-3 PUFA bolsters progeny immunocompetence through enhanced passive immunity and antibody titres against routine vaccination. In conclusion, it appears that chicks may benefit from the incorporation of n-3 PUFA in the breeder diets; however, little attention is paid to fatty acids composition in breeder nutrition. We also highlight gaps in knowledge and future research perspectives.

Effect of dietary n-3 polyunsaturated fatty acids on the composition of cecal microbiome of Lohmann hens

Supplementation of n-3 fatty acids to poultry diets is widely acknowledged for its role in enhancing poultry products, however, little is known about the compositional responses of gut microbial communities to type and dosage of these supplements.  Here, we compared the effects of n-3 polyunsaturated fatty acids (PUFA), supplied as alpha-linolenic acid (ALA) or docosahexaenoic acid (DHA), on the composition of bacterial communities in ceca of laying hens.  Corn-soybean basal diets were supplemented with either flaxseed oil (FO, ALA-rich) or marine algal biomass (MA, DHA-rich), and each supplied 0.20 and 0.60% of total n-3 PUFA in the diet.  Lohmann LSL-Classic laying hens (n = 10/treatment) were randomly allocated to one of the 4 diets.  After 8 weeks of feeding, blood, liver and cecal digesta samples were obtained for plasma glucose, fatty acids, and short chain fatty acids analyses, respectively.  The gut bacterial communities were characterized using genomic DNA extracted from cecal contents, whereby the V3-V4 hypervariable region of the 16S rRNA gene was sequenced using the Illumina Miseq® platform.  Firmicutes and Bacteroidetes were the predominant phyla in both the FO- and MA-fed groups.  The relative abundance of Tenericutes, often associated with immunomodulation, was relatively higher (P<0.0001) in the FO than MA group.  Although the relative abundance of Bacteroides was greater for the FO- than the MA-fed group, this genus was negatively correlated (P<0.05) with total n-3 PUFA in the liver at higher dosages of both FO- and MA-fed hens.  Higher dose of FO (0.60%) and both dosages of MA (0.20 and 0.60%) substantially enriched several members of Firmicutes (e.g., Faecalibacterium, Clostridium and Ruminococcus) which are known to produce butyrate.  Moreover, co-occurrence network analysis revealed that, in the FO 0.60- and MA 0.20-fed hens, Ruminococcaceae was the most influential taxon accounting for about 31% of the network complexity.  These findings demonstrate that supplementation of different type and level of n-3 PUFA in hens' diets could enrich microbial communities with potential role in lipid metabolism and health.

Diet and Gut Microbes Act Coordinately to Enhance Programmed Cell Death and Reduce Colorectal Cancer Risk

Diet is an important risk factor for colorectal cancer (CRC), and several dietary constituents implicated in CRC are modified by gut microbial metabolism. Microbial fermentation of dietary fiber produces short-chain fatty acids, e.g., acetate, propionate, and butyrate. Dietary fiber has been shown to reduce colon tumors in animal models, and, in vitro, butyrate influences cellular pathways important to cancer risk. Furthermore, work from our group suggests that the combined effects of butyrate and omega-3 polyunsaturated fatty acids (n-3 PUFA) may enhance the chemopreventive potential of these dietary constituents. We postulate that the relatively low intakes of n-3 PUFA and fiber in Western populations and the failure to address interactions between these dietary components may explain why chemoprotective effects of n-3 PUFA and fermentable fibers have not been detected consistently in prospective cohort studies. In this review, we summarize the evidence outlining the effects of n-3 long-chain PUFA and highly fermentable fiber with respect to alterations in critical pathways important to CRC prevention, particularly intrinsic mitochondrial-mediated programmed cell death resulting from the accumulation of lipid reactive oxygen species (ferroptosis), and epigenetic programming related to lipid catabolism and beta-oxidation-associated genes.

Effect of different levels of feed restriction and fish oil fatty acid supplementation on fat deposition by using different techniques, plasma levels and mRNA expression of several adipokines in broiler breeder hens

Background

Reproductive hens are subjected to a restricted diet to limit the decline in fertility associated with change in body mass. However, endocrine and tissue responses to diet restriction need to be documented.

Objective

We evaluated the effect of different levels of feed restriction, with or without fish oil supplementation, on metabolic parameters and adipokine levels in plasma and metabolic tissues of reproductive hens.

Methods

We designed an in vivo protocol involving 4 groups of hens; RNS: restricted (Rt) unsupplemented, ANS: ad libitum (Ad, receiving an amount of feed 1.7 times greater than animals on the restricted diet) unsupplemented, RS: Rt supplemented, and AS: Ad supplemented. The fish oil supplement was used at 1% of the total diet composition.

Results

Hens fed with the Rt diet had a significantly (P < 0.0001) lower growth than Ad hens, while the fish oil supplementation had no effect on these parameters. Furthermore, the bioelectrical impedance analysis (BIA) and the fat ultrasonographic examinations produced similar results to the other methods that required animals to be killed (carcass analysis and weight of adipose tissue). In addition, the Rt diet significantly (P < 0.05) decreased plasma levels of triglycerides, phospholipids, glucose and ADIPOQ, and fish oil supplementation decreased plasma levels of RARRES2. We also showed a positive correlation between insulin values and ADIPOQ or NAMPT or RARRES2 values, and a negative correlation of fat percentage to RARRES2 values. Moreover, the effects of the Rt diet and fish oil supplementation on the mRNA expression depended on the factors tested and the hen age.

Conclusions

Rt diet and fish oil supplementation are able to modulate metabolic parameters and the expression of adipokines and their receptors in metabolic tissue.

Managing gut health without reliance on antimicrobials in poultry

It is well established that antimicrobials in animal feed enhance feed efficiency, promote animal growth and improve the quality of animal products. However, resistance development in bacterial populations, and hence consumer demand for products free of antimicrobial residues, has prompted efforts to develop alternatives that can replace antimicrobials without causing loss of productivity or product quality. One of the key barriers to complete withdrawal from antimicrobial use is microbial infection, for example, necrotic enteritis. There is much interest in using in-feed nutraceuticals such as prebiotics, probiotics, organic acids and plant extracts as alternatives to antimicrobials to create a healthy gastrointestinal environment and to prevent and treat enteric infections. Enzymes are generally used to alleviate anti-nutritional factors in feed, but there is growing awareness of their beneficial effects on the gastrointestinal environment, and consequently on gut health. An example of this is production of prebiotic xylo-oligosaccharides when xylanase is added to feed. This review discusses developments in alternatives to antimicrobials that can aid in managing gut health in a post-antimicrobial era, with particular reference to recent nutritional strategies.

Influence of dietary supplementation with flaxseed and lactobacilli on the mucosal morphology and proliferative cell rate in the jejunal mucosa of piglets after weaning

The aim of the study was to investigate the influence of flaxseed and lactobacilli supplementation to the diet of piglets during the time period between 10 days before and 21 days after weaning. The morphometry of the jejunal mucosa and proliferative ratio of both epithelial and lamina propria cells were compared with those found in a group of piglets fed with the usual diet added with sunflower oil during the same time period. The addition of flaxseed oil to the diet significantly increased the crypt depth in comparison with both groups supplemented with sunflower (P < 0.05 and 0.001 respectively) on the weaning day. Moreover, the flaxseed addition caused a significant decrease in villus height (P < 0.01) and crypt depth (P < 0.01) 21 days postweaning in comparison with the sunflower group. The proliferative ratio of the epithelial cells in the sunflower group on the weaning day was significantly higher than in both flaxseed groups (P < 0.01). Paradoxically, significantly higher proliferative activity in the mucosal connective tissue in the group with flaxseed supplementation in comparison with the sunflower group was observed on the day of weaning, as well as 3 days later (P < 0.05 both). A combination of flaxseed with lactobacilli showed significantly lower proliferative activity in the connective tissue cells from weaning up to 7 days after weaning (P < 0.05 all) in comparison with the flaxseed group.

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives

Background

Poultry remains a major source of foodborne bacterial infections. A variety of additives with presumed anti-microbial and/or growth-promoting effects are commonly added to poultry feed during commercial grow-out, yet the effects of these additives on the gastrointestinal microbial community (the GI microbiome) as the bird matures remain largely unknown. Here we compared temporal changes in the cecal microbiome to the effects of formic acid, propionic acid, and medium-chain fatty acids (MCFA) added to feed and/or drinking water.

Results

Cecal bacterial communities at day of hatch (n = 5 birds), 7d (n = 32), 21d (n = 27), and 42d (n = 36) post-hatch were surveyed using direct 454 sequencing of 16S rRNA gene amplicons from each bird in combination with cultivation-based recovery of a Salmonella Typhimurium marker strain and quantitative-PCR targeting Clostridium perfringens. Treatment effects on specific pathogens were generally non-significant. S. Typhimurium introduced by oral gavage at day of hatch was recovered by cultivation from nearly all birds sampled across treatments at 7d and 21d, but by 42d, S. Typhimurium was only recovered from ca. 25% of birds, regardless of treatment. Sequencing data also revealed non-significant treatment effects on genera containing known pathogens and on the cecal microbiome as a whole. In contrast, temporal changes in the cecal microbiome were dramatic, highly significant, and consistent across treatments. At 7d, the cecal community was dominated by three genera (Flavonifractor, Pseudoflavonifractor, and a Lachnospiracea sequence type) that accounted for more than half of sequences. By 21d post-hatch, a single genus (Faecalibacterium) accounted for 23-55% of sequences, and the number of Clostridium 16S rRNA gene copies detected by quantitative-PCR reached a maximum.

Conclusions

Over the 42 d experiment, the cecal bacterial community changed significantly as measured by a variety of ecological metrics and increases in the complexity of co-occurrence networks. Management of poultry to improve animal health, nutrition, or food safety may need to consider the interactive effects of any treatments with the dramatic temporal shifts in the taxonomic composition of the cecal microbiome as described here.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-014-0282-8) contains supplementary material, which is available to authorized users.

Pythium irregulare fermentation to produce arachidonic acid (ARA) and eicosapentaenoic acid (EPA) using soybean processing co-products as substrates

Arachidonic acid (ARA) and eicosapentaenoic acid (EPA) were produced by Pythium irregulare fungus using soybean cotyledon fiber and soy skim, two co-products from soybean aqueous processing, as substrates in different fermentation systems. Parameters such as moisture content, substrate glucose addition, incubation time, and vegetable oil supplementation were found to be important in solid-state fermentation (SSF) of soybean fiber, which is to be used as animal feed with enriched long-chain polyunsaturated fatty acids (PUFA). Soybean fiber with 8 % (dwb) glucose supplementation for a 7-day SSF produced 1.3 mg of ARA and 1.6 mg of EPA in 1 g of dried substrate. When soy skim was used as substrate for submerged fermentation, total ARA yield of 125.7 mg/L and EPA yield of 92.4 mg/L were achieved with the supplementation of 7 % (w/v) soybean oil. This study demonstrates that the values of soybean fiber and soy skim co-products could be enhanced through the long-chain PUFA production by fermentation.

The effects of lactoferrin on the intestinal environment of broiler chickens

The influence of in-feed lactoferrin (Lf) on bird production, intestinal microbiota, mucosal immune system and gut microarchitecture was assessed in male Cobb 500 broiler chickens. Birds were given one of four diets from day of hatch: Control (basal diet with no additives), ZnB (basal diet + 50 mg/kg zinc bacitracin), Lf 250 mg/kg (basal diet + 250 mg/kg Lf) and Lf 500 mg/kg (basal diet + 500 mg/kg Lf); n = 24 birds/treatment. An apparent metabolisable energy study was performed between d 25-32. Lf did not affect growth rate or feed conversion in the period 0-21 d of age, nor performance or energy metabolism during the 7 d metabolism experiment which commenced at 25 d of age.The profiles of caecal microbial communities were significantly different in birds given ZnB compared with birds given a diet with no additives, or supplemented with 250 mg/kg Lf. Birds given 250 mg/kg Lf also had a different microbial profile compared with birds given 500 mg/kg Lf. In comparison to control birds, Lf treated birds showed some differences in the T cell proportions in caecal tonsil and spleen. No differences in ileal villus height, crypt depth or goblet cell proportions were observed amongst dietary treatments. Whilst Lf had little effect on the measured parameters, the use of an integrated approach to study the influence of novel feed additives may facilitate a greater understanding of the relationships between nutrition, gut health and bird performance.

Dietary long-chain n-3 PUFA, gut microbiota and fat mass in early postnatal piglet development--exploring a potential interplay

Dietary n-3PUFA and gut bacteria, particularly Bacteroidetes, have been suggested to be related to adiposity. We investigated if n-3PUFA affected fat storage and cecal bacteria in piglets. Twenty-four 4-day-old piglets were allocated to formula rich in n-3PUFA (∼3E%) from fish oil (FO) or n-6PUFA from sunflower oil (SO) for 14 days. We assessed body weight, fat accumulation by dual-energy X-ray absorptiometry and microbial molecular fingerprints. Dietary PUFA-composition was reflected in higher erythrocyte n-3PUFA in the FO- than the SO-group (P<0.001). Principal component analysis revealed group differences in the overall microbiotic composition, which involved a larger Bacteroides community in the SO-group (P=0.02). There was no significant difference in body fat percentage and no relationship between fat accumulation and gut Bacteroides. Hence, this study does not support an impact of n-3PUFA or microbiota on fat accumulation during the postnatal maturation period. The impact of dietary PUFA on the gut Bacteroides warrants further investigation.

Effects of dietary lipids and Clostridium butyricum on the performance and the digestive tract of broiler chickens

The effects of two sources of dietary lipids and supplementation of Clostridium butyricum on performance and intestinal metabolism of broilers were investigated. In a 2 x 2 factorial arrangement, 168 one-day-old broiler chicks were divided into four treatment groups, and fed four diets with two lipid sources (soya bean oil or fish oil, at 25 g/kg and 30 g/kg in starter and grower diets respectively), and without or with supplementation of C. butyricum (1 x 10(9) colony forming units per kg diet). C. butyricum had no effect on broiler performance. At 20 and 40 d of age, the pH of caecal digesta and the relative length of caecum were decreased after supplementation of C. butyricum (p < 0.05). After this treatment, the activity of alkaline phosphatase was increased in jejunal mucosa at 40 d of age (p < 0.01). Furthermore, there were increases in populations of lactic acid bacteria and the concentrations of acetic acid, n-butyric acid, n-valeric acid and total short chain fatty acids in caecal digesta of birds fed C. butyricum (p < 0.05). A significant interaction between lipid source and C. butyricum was found in the pH of caecal digesta at 20 d of age (p < 0.01). The results of the present study indicated that dietary supplementation of C. butyricum maybe a benefit for gut health of broiler chickens.

Molecular fingerprints of the human fecal microbiota from 9 to 18 months old and the effect of fish oil supplementation

OBJECTIVES

The aim of this study was to monitor changes in the fecal microbiota from 9 to 18 months and to investigate the effect of increasing dietary n-3 polyunsaturated fatty acids on the fecal microbiota.

PATIENTS AND METHODS

In a double-blind controlled trial with random allocation to daily supplementation with 5 mL of fish oil (FO) or sunflower oil (SO) from 9 to 18 months of age, stool samples were collected from 132 healthy Danish infants. Molecular fingerprints of the bacterial DNA were obtained by terminal restriction fragment length polymorphism (T-RFLP).

RESULTS

The T-RFLP profiles indicated that a few T-RFs became dominant with age (bp100 and 102, both presumed to be Bacteroidetes) concomitantly with an overall increase in the microbial diversity (P = 0.04). Breast-feeding influenced both the T-RFLP profiles at 9 months and the changes from 9 to 18 months, and breast-feeding cessation during the trial modified the response to the dietary oils. In the FO group, the increase in bp102 was significantly reduced among children weaned before compared with those weaned during the trial (P = 0.027), whereas the increase in bp100 was reduced in the preweaned children of the SO group relative to those weaned during the trial (P = 0.004). This was supported by intervention group differences in the changes in bp102 and bp100 among the earlier weaned children (P = 0.06 and P = 0.09, respectively).

CONCLUSIONS

Cessation of breast-feeding played a dominant role relative to developmental changes in the fecal microbiota from 9 to 18 months. FO compared with SO supplementation affected changes in large bacterial groups, but only among children who had stopped breast-feeding before 9 months of age.