Cecal Microbiome Research Articles

Metagenomic profiling of cecal microbiota and antibiotic resistome in rodents

The rodent gut microbiota is a known reservoir of antimicrobial resistance, yet the distribution of antibiotic resistance genes (ARGs) within rodent cecal microbial communities and the specific bacterial species harboring these ARGs remain largely underexplored. This study employed high-throughput sequencing of 122 samples from five distinct rodent species to comprehensively profile the diversity and distribution of ARGs and to identify the bacterial hosts of these genes. A gene catalog of the rodent cecal microbiome was constructed, comprising 22,757,369 non-redundant genes. Analysis of the microbial composition and diversity revealed that Bacillota and Bacteroidota were the dominant bacterial phyla across different rodent species, with significant variations in species composition among the rodents. In total, 3703 putative antimicrobial resistance protein-coding genes were identified, corresponding to 392 unique ARG types classified into 32 resistance classes. The most enriched ARGs in the rodent cecal microbiome were associated with multidrug resistance, followed by glycopeptide and elfamycin antibiotics. Procrustes analysis demonstrated a correlation between the structure of the microbial community and the resistome. Metagenomic assembly-based host tracking indicated that most ARG-carrying contigs originated from the bacterial family Oscillospiraceae. Additionally, 130 ARGs showed significant correlations with mobile genetic elements. These findings provide new insights into the cecal microbiota and the prevalence of ARGs across five rodent species. Future research on a wider range of wild rodent species carrying ARGs will further elucidate the mechanisms underlying the transmission of antimicrobial resistance.

Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages.

The composition and function of the active cecal microbiome were significantly different between the plateau Tibetan chicken population and the plain chicken population. Higher expression genes related to energy metabolism and immune response were found in the cecal microbiome of the plateau Tibetan chicken population. The cecal microbiome in the plateau Tibetan chicken population exhibited higher biosynthesis of short-chain fatty and secondary bile acids, resulting in higher cecal content of these metabolites. The active Bacteroidetes/Firmicutes ratio in the cecal microbiome may contribute to the high-altitude adaptive advantage of the plateau Tibetan chicken population.

Dietary Fermented Blueberry Pomace Supplementation Improves Small Intestinal Barrier Function and Modulates Cecal Microbiota in Aged Laying Hens.

This study aimed to investigate the effects of fermented blueberry pomace (FBP) on the intestinal barrier function and cecal microbiome of aged laying hens. A total of 320 Yukou Jingfen No. 8 laying hens (345-day-old) were randomly divided into a control group, 0.25% FBP group, 0.5% FBP group, or 1.0% FBP group. The results showed that the villus height (VH) in the jejunum of the 0.25-0.5% FBP groups and villus surface area in the jejunum of the 0.25% FBP group were higher (p < 0.05), while 0.25% FBP supplementation displayed a higher (p = 0.070) VH in the ileum compared to the control group. Mucin-2 expression was upregulated (p < 0.05) in the jejunum of the 0.5% FBP group and the ileum of the 0.25-0.5% FBP groups. Compared to the control group, interleukin (IL)-4 and IL-13 expressions were upregulated (p < 0.05) in the 1.0% FBP group. Microbiota analysis revealed that Prevotella abundance in the cecum of the 0.5-1.0% FBP groups was higher (p < 0.05) than in the 0.25% FBP group. In addition, microbial function prediction analysis showed that cecal microbiota in the 0.25% FBP group were mainly enriched by alanine/aspartate/glutamate metabolism and methane metabolism. Moreover, Spearman's correlation analysis revealed the potential correlations between the abundance of the cecal microbiota and intestinal-barrier-function-related gene expressions, as well as the short-chain fatty acid content, of laying hens. In summary, dietary FBP supplementation enhanced intestinal barrier function by improving intestinal morphology, upregulating gene expressions related to barrier function, and altering the cecal microbiota of aged laying hens.

Partially hydrolyzed guar gum suppresses binge alcohol-induced liver fat accumulation via gut environment modulation in mice.

Alcohol-associated liver disease (ALD), including alcoholic fatty liver, is a serious problem in many countries, and its economic costs to society are enormous. There is evidence indicating the relations between gut environments and liver disease, and thus, improvement of gut environment is expected to be an effective approach for ALD prevention. In this study, we explored the preventive effect of partially hydrolyzed guar gum (PHGG) on ALD focusing on the gut-liver axis. Two weeks of PHGG pre-feeding suppressed the liver fat accumulation in the experimental binge alcohol model mouse. In cecal microbiome, PHGG pre-feeding increased beneficial Bifidobacterium with its metabolite acetate concentration and suppressed the alcohol-induced increase in the potential pathobiont Streptococcus. PHGG pre-feeding increased colonic gene expression of angiogenin genes, which act as antimicrobial peptides and decreased expression of genes for mast cell protease, which suggests a potential involvement in leaky gut. Correlation network analysis based on evaluated parameters revealed four relations worth noticing. (i) The abundance of Bifidobacterium positively correlated with cecal acetate. (ii) Cecal acetate negatively correlated with Streptococcus via colonic angiogenin expression. (iii) Streptococcus positively correlated with liver fat area. (iv) Cecal acetate had direct negative correlation with liver fat area. Considering these relations comprehensively, acetate produced by Bifidobacterium may be a key mediator in ALD prevention; it inhibited growth of potential pathobiont Streptococcus and also directly regulated liver lipid metabolism reaching through portal vein. This study demonstrated that regularly intake of PHGG may be effective in reducing the risk of alcoholic fatty liver via gut-liver axis.

Probiotic strategies for mitigating heat stress effects on broiler chicken performance.

The primary objective of this study was to evaluate the effects of liquid (Fructose-added lactic acid bacteria, F-LAB) and commercial (Commercial LAB, C-LAB) probiotics sourced from Rye-Grass Lactic Acid Bacteria (LAB) on broiler chickens experiencing heat stress (HS). The research involved 240 broiler chicks, divided into six groups: control, F-LAB, C-LAB (raised at 24°C), HS, F-LAB/HS, and C-LAB/HS (exposed to 5-7h of 34-36°C daily). The study followed a randomized complete block design, with each group consisting of 40 chicks. F-LAB and HS/F-LAB groups received a natural probiotic added to their drinking water at a rate of 0.5ml/L, while C-LAB and HS/C-LAB groups were supplemented with a commercial probiotic at the same dosage. Control and HS groups received no probiotic supplementation. The duration of the study was 42days, with data collected on growth performance, feed intake, feed conversion ratio, and health parameters. Statistical analyses were performed using ANOVA, and significant differences between groups were determined using post hoc tests. The results revealed that without probiotic supplementation, heat stress led to a decrease in body weight gain, T3 levels, citrulline, and growth hormone levels, along with an increase in the feed conversion ratio, serum corticosterone, HSP70, ALT, AST, and leptin levels (p < 0.05 for all). Heat stress also adversely affected cecal microbiota, reducing lactic acid bacteria count (LABC) while increasing Escherichia coli and coliform bacteria (CBC) counts. However, in the groups receiving probiotic supplementation under heat stress (F-LAB/HS and C-LAB/HS), these effects were alleviated (p < 0.05 for all). Particularly noteworthy was the observation that broiler chickens supplemented with natural lactic acid bacteria (F-LAB) exhibited greater resilience to heat stress compared to those receiving the commercial probiotic, as evidenced by improvements in growth, liver function, hormonal balance, intestinal health, and cecal microbiome ecology (p < 0.05). These findings suggest that the supplementation of naturally sourced probiotics (F-LAB) may positively impact the intestinal health of broiler chickens exposed to heat stress, potentially supporting growth and health parameters.

Positive Intervention of Distinct Peptides in Clostridioides difficile Infection in a Mouse Model

Clostridioides difficile infection (CDI) is a common healthcare-associated infection and the leading cause of gastroenteritis-related deaths worldwide. To investigate the effects of peptide composition of different protein products on CDI, we analyzed and compared the peptide sequences and compositions from Engraulis japonicus and Glycine max using Ultra High Performance Liquid Chromatography Tandem Mass Spectrometry (UPLC-MS/MS). An animal model of CDI was also established to investigate the potential therapeutic effects of these peptides in vivo. The peptide compositions of E. japonicus and G. max differed, with only 11% of the peptide sequences being identical. Oral administration of the tested peptides could reduce intestinal inflammation, repair the intestinal barrier, increase the proportion of beneficial bacteria, and reduce the proportion of harmful bacteria, providing a therapeutic effect against CDI. However, the peptides may differ considerably in some aspects. E. japonicus peptides were superior to G. max peptides in promoting colon epithelial cell proliferation and repairing tight intestinal cell junctions. Interestingly, the two sources of peptides have different effects on the cecal microbiome. E. japonicus peptides can effectively restore the diversity and richness of intestinal microbiota, while G. max peptides have poor regulatory effects on the intestinal microbiota structure. Overall, E. japonicus peptides showed better results than G. max peptides in treating CDI. This study supports the potential treatment of CDI with natural peptides and promotes the development of specialty foods for CDI enteritis. Clostridioides difficile infection (CDI) is a common healthcare-associated infection and the leading cause of gastroenteritis-related deaths worldwide. To investigate the effects of peptide composition of different protein products on CDI, we analyzed and compared the peptide sequences and compositions from Engraulis japonicus and Glycine max using Ultra High Performance Liquid Chromatography Tandem Mass Spectrometry (UPLC-MS/MS). An animal model of CDI was also established to investigate the potential therapeutic effects of these peptides in vivo. The peptide compositions of E. japonicus and G. max differed, with only 11% of the peptide sequences being identical. Oral administration of the tested peptides could reduce intestinal inflammation, repair the intestinal barrier, increase the proportion of beneficial bacteria, and reduce the proportion of harmful bacteria, providing a therapeutic effect against CDI. However, the peptides may differ considerably in some aspects. E. japonicus peptides were superior to G. max peptides in promoting colon epithelial cell proliferation and repairing tight intestinal cell junctions. Interestingly, the two sources of peptides have different effects on the cecal microbiome. E. japonicus peptides can effectively restore the diversity and richness of intestinal microbiota, while G. max peptides have poor regulatory effects on the intestinal microbiota structure.

PSVI-5 Bacteriophage biocontrol of avian pathogenic Escherichia coli in laying hens does not produce collateral effects on the cecal microbiota

Abstract Bacteriophages have shown promise as an alternative to antibiotics for managing or preventing avian pathogenic Escherichia coli (APEC) in the egg industry. In a previous study, a phage cocktail comprising 3 virulent phages was shown to prevent APEC infections in laying hens. The aim of this study was to investigate whether orally and intramuscularly administered phages affect the intestinal barrier function of chickens, with a focus on cecal microbiome. In a 4-d trial, a total of 35 laying hens were randomly assigned to one of four treatment groups: 1) Medium control group (bacterial broth + phage buffer), 2) APEC only control (APEC + buffer); 3) IM group (Phage +APEC), or 4) DW group (phage in drinking water (4 d prior to APEC + APEC). Cecum samples were subjected to 16S rRNA gene sequencing targeting the V4 region to assess the effects of phages on cecal bacterial diversity. A 1-way ANOVA was used to evaluate alpha diversity with respect to treatment and time. Microbial community structure was analyzed using β-dispersion and permutational multivariate analysis of variance (PERMANOVA) to determine the effect of each treatment. Significant (P &amp;lt; 0.05) differentially abundant genera were identified with DESeq2 by fitting a negative binomial model to each treatment vs treatment comparison (“~Treatment”). Across the treatment and control groups, 13 phyla were identified. Firmicutes (53.81%), Bacteroidota (23.83%), Actinobacteriota (1.84%), and Proteobacteria (1.02%) were the most abundant phyla among the amplicon sequence variants (ASVs), with 18.39% being unclassified. Neither richness (P = 0.448) nor Shannon diversity (P = 0.687) exhibited significance in α- diversity metric between treatment and control groups. β-dispersion analysis showed no significant difference (P = 0.239) between treatment and control groups, indicating similar bacterial variability among groups. Moreover, the β-diversity representing microbiota structure was not affected by any phage treatment (P = 0.083). In each treatment group, 76 unique genera were identified, with Megamonas (15.80 %), Lactobacillus (8.76%), Faecalibacterium (7.70 %), Megasphaera (1.58%), Alloprevotella (1.54%), [Ruminococcus] torques group (1.29%), Prevotellaceae UCG-001 (1.14%), Bifidobacterium (1.04%), and Olsenella (0.48%) being the most abundant. Notably, Lactobacillus was more abundant (~ 10 to 20%) in medium control group compared with phage treated and APEC only treatment groups. Furthermore, gene expression profiles of various genera (pairwise) were analyzed using log2 fold change (log2FC), revealing differences (P &amp;lt; 0.05) between control and treatment groups for a total of 58 genera. It was concluded that bacteriophage selectively killed APEC population without comprising the population and structure of cecal microbiome in laying hens.

Chronological dynamics of the gut microbiome in response to the pasture grazing system in geese.

It is commonly accepted that dietary fibers are good for gut health. The effect of fibers on the diversity and metabolic activities of the cecal microflora, however, differ with the passage of time. Therefore, we investigated the time-series impacts of the pasture grazing system (a high dietary fiber source) on the cecal microbiome and short-chain fatty acids in Wanpu geese, comparing it to commercial feeding (a low dietary fiber source). The cecal microbiota composition and SCFA concentrations were evaluated by 16S rRNA gene sequencing and gas chromatography, respectively. We found that pasture produced a generally quick positive response to Bacteroidales, Lactobacillales, Gastranaerophilales (at 45 days), Lachnospirales, and Oscillospirales (at 60 days and 90 days) irrespective of Erysipelotrichales (at 45 days), Clostridia_UCG-014, RF39 (at 60 days), Christensenellales, and Peptostreptococcales-Tissierellales (at 90 days) in geese. Meanwhile, we found that Lactobacillales, Gastranaerophilales, Lachnospirales, and Oscillospirales were significantly correlated with short-chain fatty acids in pasture grazing geese. Indeed, the correlation of cecal microbiota with SCFAs led to altered microbial functions evinced by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases. This study emphasizes the importance of dietary fiber sources in influencing beneficial impacts in regulating geese microbiota homeostasis and metabolic functions such as energy and lipid metabolism.IMPORTANCELow dietary fiber diet sources cause gut microbial and short-chain fatty acid alterations that lead to compromised animal health. The establishment of an artificial pasture grazing system at the expense of ryegrass is a good source of dietary fiber for geese. Our results described the importance of pasture in maintaining the gut microbiota, SCFAs, and potential microbial functions reported by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases.

Placental and fetal enrichment of microplastics from disposable paper cups: implications for metabolic and reproductive health during pregnancy

The disposable paper cups (DPCs) release millions of microplastics (MPs) when used for hot beverages. However, the tissue-specific deposition and toxic effects of MPs and associated toxins remain largely unexplored, especially at daily consumption levels. We administered MPs and associated toxins extracted from leading brand DPCs to pregnant mice, revealing dose-responsive harmful effects on fetal development and maternal physiology. MPs were detected in all 13 examined tissues, with preferred depositions in the fetus, placenta, kidney, spleen, lung, and heart, contributing to impaired phenotypes. Brain tissues had the smallest MPs (90.35 % < 10 µm). A dose-responsive shift in the cecal microbiome from Firmicutes to Bacteroidetes was observed, coupled with enhanced biosynthesis of microbial fatty acids. A moderate consumption of 3.3 cups daily was sufficient to alter the cecal microbiome, global metabolic functions, and immune health, as reflected by tissue-specific transcriptomic analyses in maternal blood, placenta, and mammary glands, leading to neurodegenerative and miscarriage risks. Gene-based benchmark dose framework analysis suggested a safe exposure limit of 2 to 4 cups/day in pregnant mice. Our results highlight tissue-specific accumulation and metabolic and reproductive toxicities in mice at DPC consumption levels presumed non-hazardous, with potential health implications for pregnant women and fetuses.

Investigation into the supplementation of a ferric sillen core-linked polymer on the health and physiological performance of broiler chickens

Poultry is a ubiquitous and highly sought-after protein source valued for its accessibility, notable protein content, and lack of religious constraints. However, the demand for poultry has resulted in a surge in intensive production practices. The transition from subsistence agricultural practices to intensive food production resulted in the widespread adoption of antibiotics for both therapeutic and economic purposes. These interventions were intended to enhance meat yield, promote bird health, and enhance cost-effectiveness of production. However, this inadvertently contributed to the rise of antimicrobial resistance (AMR). Therefore, the need to explore alternative approaches to mitigate the problems associated with AMR has become increasingly pressing. In response, metal-based compounds have emerged as a promising substitute to conventional antibiotics. In this study, the effects of a water soluble metallo-antimicrobial supplement, ferric sillen core-linked polymer (FSCLP), on body weight gain, feed conversion, water intake, volatile fatty acid (VFA) production, cecal microbiome and intestinal morphology in broilers was examined. The findings of this study suggested that the addition of the FSCLP resulted in better bird performance, even during a period of heat stress. Volatile fatty acids (VFA) analysis of cecal contents indicated that there were significantly higher levels (p < 0.05) of butyric and valeric acids. Cecal microbiome analysis confirmed significantly lower abundance (p < 0.05) of Proteobacteria (e.g., E. coli) and a significantly greater abundance of VFA-producing bacteria such as Intestinimonas butyriciproducens, Blautia and Lachnospiraceae. The intestinal morphology data showed supplementation with the FSCLP at 80 ppm resulted in a significantly higher (p < 0.05) villus height of the jejunum.This study emphasises the potential of FSCLP as a feasible solution to the issues faced by AMR in chicken production, providing insights into its beneficial impacts on performance, microbial composition, and intestinal health.

Immune modulation and cecal microbiome changes in broilers fed with fenugreek seeds and Bacillus-based probiotics

Intensive broiler production systems face challenges like enteric diseases, impacting global food security. Strategies to enhance broiler immunity and gut health, particularly amidst antibiotic growth promoter restrictions, are crucial. The present study investigated the combined effects of fenugreek seeds (FS) and Bacillus-based direct-fed microbials (DFM) on immune-related gene expression in the ileum and alteration of microbial population in the cecum of broiler. The study involved 160 Ross 308 broiler chicks, which were divided into four groups consisting of 5 replicates, each containing eight birds. The chicks were grown for a period of 42 d, during which they had ad libitum access to feed and water. Dietary treatments were: Control (basal diet), FS5 (basal + 5g/kg fenugreek seeds), FS5DFM (basal + 5g/kg fenugreek seeds + 0.1g/kg Bacillus-based DFM), and DFM (basal + 0.1g/kg Bacillus-based DFM). Ileum tissue and cecal contents were collected on d 42 for gene expression and gut microbiome analysis. Ileal gene expression analysis revealed the downregulation of IL-6, IL-8L2, CASP6, PTGS2, and IRF7 in both FSs and DFMs groups compared to the control, suggesting individual immunomodulatory effects. However, avian β-defensin genes exhibited complex regulation, highlighting the need for further investigation. Cecal microbiome diversity remained stable, with subtle shifts in specific taxa influenced by FSs and DFMs. Interestingly, the combination of the FSs and DFMs uniquely impacted specific taxa, including Clostridiales vadin BB60. These findings suggest that both FSs and DFMs demonstrated potential for improving broiler immunity through inflammation reduction. The combination of FSs and DFMs offers a synergistic effect in immune modulation and specific microbial modulation, warranting further investigation with pathogen challenge models for comprehensive understanding.

Infant Microbiota Communities and Human Milk Oligosaccharide Supplementation Independently and Synergistically Shape Metabolite Production and Immune Responses in Healthy Mice

BackgroundMultiple studies have demonstrated associations between the early-life gut microbiome and incidence of inflammatory and autoimmune disease in childhood. Although microbial colonization is necessary for proper immune education, it is not well understood at a mechanistic level how specific communities of bacteria promote immune maturation or drive immune dysfunction in infancy. ObjectivesIn this study, we aimed to assess whether infant microbial communities with different overall structures differentially influence immune and gastrointestinal development in healthy mice. MethodsGerm-free mice were inoculated with fecal slurries from Bifidobacterium longum subspecies infantis positive (BIP) or B. longum subspecies infantis negative (BIN) breastfed infants; half of the mice in each group were also supplemented with a pool of human milk oligosaccharides (HMOs) for 14 d. Cecal microbiome composition and metabolite production, systemic and mucosal immune outcomes, and intestinal morphology were assessed at the end of the study. ResultsThe results showed that inoculation with a BIP microbiome results in a remarkably distinct microbial community characterized by higher relative abundances of cecal Clostridium senu stricto, Ruminococcus gnavus, Cellulosilyticum sp., and Erysipelatoclostridium sp. The BIP microbiome produced 2-fold higher concentrations of cecal butyrate, promoted branched short-chain fatty acid (SCFA) production, and further modulated serotonin, kynurenine, and indole metabolism relative to BIN mice. Further, the BIP microbiome increased the proportions of innate and adaptive immune cells in spleen, while HMO supplementation increased proliferation of mesenteric lymph node cells to phorbol myristate acetate and lipopolysaccharide and increased serum IgA and IgG concentrations. ConclusionsDifferent microbiome compositions and HMO supplementation can modulate SCFA and tryptophan metabolism and innate and adaptive immunity in young, healthy mice, with potentially important implications for early childhood health.

The Brominated Flame Retardant Hexabromocyclododecane Causes Systemic Changes in Polyunsaturated Fatty Acid Incorporation in Mouse Lipids.

Brominated flame retardants are used in many household products to reduce flammability, but often leach into the surrounding environment over time. Hexabromocyclododecane (HBCD) is one brominated flame retardant detected in human blood across the world. HBCD exposure can result in neurological problems and altered lipid metabolism, but to date the two remain unlinked. As lipids constitute ∼50% of brain dry weight, lipid metabolism plays a critical role in neuronal function and homeostasis. To determine the effect of HBCD exposure on brain lipid metabolism, young adult male C57BL/6 mice were exposed to 1 mg/kg HBCD every 3 days for 28 days. Major lipid classes were found to change across brain regions, including the membrane glycerolipids phosphatidylcholine and phosphatidylethanolamine, and sphingolipids such as hexosylceramide. In addition, saturated, monounsaturated, and polyunsaturated fatty acids were enriched within brain lipid species. To understand the source of the brain lipidomic alterations, the blood and liver lipidomes and the cecal microbiome were evaluated. The liver and blood demonstrated changes amongst multiple lipid classes, including triacylglycerol suppression, as well as altered esterified fatty acid content. Significant alterations were also detected in the cecal microbiome, with decreases in the Firmicutes to Bacteriodetes ratio, changes in beta diversity, and pathway alterations associated with metabolic pathways and amino acid biosynthesis. These data demonstrate that HBCD can induce lipidomic alterations across brain regions and organs and supports a potential role of the microbiome in these alterations.

Comparison of Chinese medicine additives for antibiotic resistance risks in the Wuding chickens under high stocking density: Advantages and drawbacks

Traditional Chinese medicines (TCMs) with anti-pathogenic properties have been increasingly utilized in animal husbandry as substitutes for antibiotics. However, lingering uncertainties persist regarding the mobility, bacterial hosts, and potential human hazards associated with antibiotic resistance genes (ARGs) in animal husbandry when TCMs are introduced. In this study, cecal digesta from Wuding chickens subjected to varying stocking densities (moderate and high) and treated with different TCMs (dihydroartemisinin, berberine hydrochloride, and oligomeric proanthocyanidins) were collected and subjected to metagenomics-based analysis. A total of 280 ARG subtypes were identified, with multidrug and aminoglycoside resistance genes being the most diverse and abundant. The primary antibiotic resistance bacteria identified belonged to the phyla of Firmicutes (38.68%), Bacteroidetes (22.74%), and Proteobacteria (12.71%); however, some pathogenic antibiotic-resistant bacteria (PARB) were also identified across different samples. Surprisingly, high stocking density was not observed to propagate ARGs, which could be due to the restricted usage of antibiotics. Furthermore, higher proportions of mobile genetic elements and some multidrug-resistant PARB (∼4 times) were observed in high-stocking-density chickens fed berberine hydrochloride than in high-stocking-density chickens fed other TCMs, which could facilitate the horizontal gene transfer (HGT) of ARGs and pose potential human health risks. In contrast, dihydroartemisinin reduced the total abundance of ARGs and the resistome risks to human health (∼10% decrease compared to control). Moreover, rank I ARGs with higher human health risk and the risk index based on ARG risk also ranked lowest (p < 0.05) in high-stocking-density chickens fed dihydroartemisinin. The reduction effect of dihydroartemisinin was achieved by regulating the cecal microbiome of broilers and inhibiting HGT (reducing the contribution from 17.7% to 4.0%). This study provides metagenomic evidence of the development of ARGs in broiler breeding environments. The findings highlight the distinct characteristics of TCMs as feed additives on regulating the antibiotic resistome during broiler farming and demonstrate dihydroartemisinin as an effective additive complying with the environmental safety.

Effects of different energy levels in low-protein diet on liver lipid metabolism in the late-phase laying hens through the gut-liver axis

BackgroundThe energy/protein imbalance in a low-protein diet induces lipid metabolism disorders in late-phase laying hens. Reducing energy levels in the low-protein diet to adjust the energy-to-protein ratio may improve fat deposition, but this also decreases the laying performance of hens. This study investigated the mechanism by which different energy levels in the low-protein diet influences liver lipid metabolism in late-phase laying hens through the enterohepatic axis to guide feed optimization and nutrition strategies. A total of 288 laying hens were randomly allocated to the normal-energy and normal-protein diet group (positive control: CK) or 1 of 3 groups: low-energy and low-protein diet (LL), normal-energy and low-protein diet (NL), and high-energy and low-protein diet (HL) groups. The energy-to-protein ratios of the CK, LL, NL, and HL diets were 0.67, 0.74, 0.77, and 0.80, respectively.ResultsCompared with the CK group, egg quality deteriorated with increasing energy intake in late-phase laying hens fed low-protein diet. Hens fed LL, NL, and HL diets had significantly higher triglyceride, total cholesterol, acetyl-CoA carboxylase, and fatty acid synthase levels, but significantly lower hepatic lipase levels compared with the CK group. Liver transcriptome sequencing revealed that genes involved in fatty acid beta-oxidation (ACOX1, HADHA, EHHADH, and ACAA1) were downregulated, whereas genes related to fatty acid synthesis (SCD, FASN, and ACACA) were upregulated in LL group compared with the CK group. Comparison of the cecal microbiome showed that in hens fed an LL diet, Lactobacillus and Desulfovibrio were enriched, whereas riboflavin metabolism was suppressed. Cecal metabolites that were most significantly affected by the LL diet included several vitamins, such as riboflavin (vitamin B2), pantethine (vitamin B5 derivative), pyridoxine (vitamin B6), and 4-pyridoxic acid.ConclusionA lipid metabolism disorder due to deficiencies of vitamin B2 and pantethine originating from the metabolism of the cecal microbiome may be the underlying reason for fat accumulation in the liver of late-phase laying hens fed an LL diet. Based on the present study, we propose that targeting vitamin B2 and pantethine (vitamin B5 derivative) might be an effective strategy for improving lipid metabolism in late-phase laying hens fed a low-protein diet.

Bacteroidales reduces growth rate through serum metabolites and cytokines in Chinese Ningdu yellow chickens

Increasing evidence has indicated that the gut microbiome plays an important role in chicken growth traits. However, the cecal microbial taxa associated with the growth rates of the Chinese Ningdu yellow chickens are unknown. In this study, shotgun metagenomic sequencing was used to identify cecal bacterial species associated with the growth rate of the Chinese Ningdu yellow chickens. We found that nine cecal bacterial species differed significantly between high and low growth rate chickens, including three species (Succinatimonas hippei, Phocaeicola massiliensis, and Parabacteroides sp. ZJ-118) that were significantly enriched in high growth rate chickens. We identified six Bacteroidales that were significantly enriched in low growth rate chickens, including Barnesiella sp. An22, Barnesiella sp. ET7, and Bacteroidales bacterium which were key biomarkers in differentiating high and low growth rate chickens and were associated with alterations in the functional taxa of the cecal microbiome. Untargeted serum metabolome analysis revealed that 8 metabolites showing distinct enrichment patterns between high and low growth rate chickens, including triacetate lactone and N-acetyl-a-neuraminic acid, which were at higher concentrations in low growth rate chickens and were positively and significantly correlated with Barnesiella sp. An22, Barnesiella sp. ET7, and Bacteroidales bacterium. Furthermore, the results suggest that serum cytokines, such as IL-5, may reduce growth rate and are related to changes in serum metabolites and gut microbes (e.g., Barnesiella sp. An22 and Barnesiella sp. ET7). These results provide important insights into the effects of the cecal microbiome, serum metabolism and cytokines in Ningdu yellow chickens.

Inositol and taurine ameliorate abnormal liver lipid metabolism induced by high sucrose intake

Previous attempts to limit fat intake failed to reduce metabolic syndrome incidence, spotlighting excessive sucrose consumption phenomenon. Recent studies challenge the traditional belief, actually fructose is predominantly metabolized in the small intestine, not just the liver. Evidence supports sucrose overconsumption leads to hepatic lipid accumulation via gut microbiome modulation, but the mechanisms and prevention strategies remain unclear. This study investigates the impact of osmolytes inositol and taurine, which are abundant in citrus fruits and seafood respectively, on lipid metabolism in rats consuming excessive sucrose. Five-week-old male Wistar rats fed with control diet, high sucrose diet, and high sucrose diet with inositol or taurine for 28 days. High sucrose diet-induced accumulation of hepatic triglyceride level was reduced only by inositol. Both inositol and taurine decreased hepatic SREBP1, ChREBP, lipogenesis enzymes mRNA levels increased by a high sucrose diet. Taurine also significantly increased the fatty acid uptake major player CD36 mRNA levels in liver. Expression of genes related to fatty acid degradation and transport remained unchanged. In cecal microbiome, high sucrose diet groups showed a decrease in alpha diversity and diverged in beta diversity from the starch diet group, while inositol and taurine did not significantly affect these aspects. Ten bacterial features including genera such as Bacteroides, Parabacteroides, Odoribacter, Streptococcus, etc., were filtered out related to the ameliorative effects of inositol and taurine on lipid metabolism. Overall, both inositol and taurine modulated hepatic lipogenesis and microbiome. However, due to taurine's enhancement of fatty acid uptake, only inositol improved steatosis in high sucrose diet rats.

Effects of herbal dregs supplementation of Salvia miltiorrhiza and Isatidis Radix residues improved production performance and gut microbiota abundance in late-phase laying hens.

The present study was designed to evaluate the effect of a mixture of Chinese medicinal residues (CMRs) consisting of Salvia miltiorrhiza residues (SMR) and Isatidis Radix residues (IRR) on productive performance, egg quality, serum lipid and hormone levels, liver and blood antioxidant capacity, oviduct inflammation levels, and gut microbiota in the late-laying stage. A total of 288 fifty-four-week-old BaShang long-tailed hens were divided into four groups. The feed trial period was 8 weeks. The control group was fed the basic diet as a CCMR group, supplemented with 3, 4, and 6% for the experimental groups LCMR, MCMR, and HCMR. The egg production rate of the MCMR group was 8.1% higher than that of the CCMR group (p < 0.05). Serum triglyceride (TG) levels of hens of the CMR-supplemented group were significantly decreased than those of the CCMR group (p < 0.05). The group supplemented with different levels of CMR had significantly higher serum HDL-C levels compared with the control group (p < 0.05). Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) levels were remarkably increased for the LCMR and MCMR groups and significantly decreased for the HCMR group compared to CCMR (p < 0.05). Serum and liver glutathione peroxidase (GSH-PX) activities were significantly increased, and malondialdehyde (MDA) levels were significantly decreased in the MCMR group compared to the CCMR group (p < 0.05). The expression levels of tubal inflammatory factor markers (IL-4, IL-1β, TNF-α) in the MCMR and HCMR groups were consistent with the pathological findings of the sections. As for cecal microbiota, supplementation with CMR affected the alpha diversity of the cecum microbiome at the genus level. The Shannon index was significantly higher in the MCMR group than in the CCMR and HCMR groups (p < 0.05). Supplementation with different levels of CMR mainly regulated the ratio of intestinal Firmicutes to Bacteroidetes and the abundance of phyla such as Proteobacteria. In addition, CMR supplementation at different levels in the diet enriched lipid-metabolizing bacteria, such as Bacteroides and Ruminococcus_gnavus_group. Furthermore, according to linear discriminant analysis (LDA) effect size (LEfSe) analysis, the MCMR group showed an increase in the number of short-chain fatty acid-producing bacteria Romboutsia and fiber-degrading specialized bacteria Monoglobus. Therefore, supplementation of appropriate amounts of CMR to the diet of laying hens enhanced reproductive hormone levels, hepatic antioxidant capacity, and lipid metabolism, alleviated the levels of oviductal inflammatory factors, and modulated the abundance structure of bacterial flora to improve the late-laying performance and egg quality. The results of the current study showed that CMR is a beneficial feed supplement for chickens when added in moderation.

Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis.

The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community's variants in chickens' ceca and to explore the most significant association between the microbiome compositions and poultry farming productivity. The meta-analysis included original data from 8 control broiler chicken groups fed with a standard basic diet and 32 experimental groups supplemented with various feed additives. Standard Illumina 16S-RNA gene sequencing technology was used to characterize the chicken cecal microbiome. Zootechnical data sets integrated with the European Production Effectiveness Factor (EPEF) were collected. Analysis of the bacterial taxa abundance and co-occurrence in chicken cecal microbiomes revealed two alternative patterns: Bacteroidota-dominated with decreased alpha biodiversity; and Bacillota-enriched, which included the Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota phyla members, with increased biodiversity indices. Bacillota-enriched microbiome groups showed elevated total feed intake (especially due to the starter feed intake) and final body weight, and high EPEF values, while Bacteroidota-dominated microbiomes were negatively associated with poultry farming productivity. The meta-analysis results lay the basis for the development of chicken growth-promoting feed supplementations, aimed at the stimulation of beneficial and inhibition of harmful bacterial patterns, where relevant metagenomic data can be a tool for their control and selection.

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.