Nest architecture in social insects is often viewed as a static structural component providing shelter or storage1. However, the extent to which these constructed environments actively shape biological traits remains poorly understood. Although the genetic and nutritional drivers of honey bee caste determination are well established2-4, the role for specialized queen cells has largely been attributed to spatial or structural factors, overlooking the influence of the physicochemical microenvironment5. Here we show that worker construction behaviour actively engineers a physicochemical niche that is crucial for queen development in honey bees. Queen cells exhibit distinct mechanical and chemical signatures that differ markedly from those of worker cells. These properties are not an accidental by-product of worker cell construction: workers construct queen cells deliberately and, in doing so, undergo task-specific physiological and transcriptomic reprogramming that enables precise engineering of these cell properties. Experimental manipulations of the rearing environment demonstrate that these physicochemical cues are causally required for normal queen development, functioning as a critical checkpoint that can profoundly influence an individual larva's development. Together, our results establish a direct mechanistic link between social construction behaviour and developmental plasticity, revealing how an engineered environment can channel organismal fate.

The ubiquitous presence of modified mycotoxins such as zearalenone-14-glucoside (ZEN-14G) in agricultural resources presents a critical challenge to livestock safety, specifically regarding their capacity to disrupt lipid metabolism and fermentation in the rumen. This study aimed to evaluate the dose- and time-dependent direct effects of ZEN-14G on rumen fermentation characteristics, nutrient disappearance, and mycotoxin biotransformation under controlled in vitro conditions, and to explore the associated microbial and metabolic responses. An in vitro batch fermentation system was established with three ZEN-14G doses, namely control (CON), low dosage (GL), and high dosage (GH), across three time points (6, 12, and 24 h). Basic fermentation parameters, fat disappearance rates, and ZEN-14G metabolites were quantified, while 16S rRNA gene sequencing and untargeted metabolomics were conducted specifically on 24 h endpoint samples from the CON and GH groups to investigate downstream mechanistic disruptions. The results showed that while baseline pH homeostasis remained unaffected across groups, ZEN-14G dose-dependently inhibited fat disappearance, with the GH group exhibiting a significant reduction throughout fermentation. Targeted quantification confirmed that ZEN-14G was predominantly deglucosylated to free ZEN and reduced to α/β-ZEL. Endpoint multi-omics revealed that although overall α/β-diversity was maintained at 24 h, ZEN-14G induced fine-scale strain-level replacement (12% shared ASVs), marked by the depletion of the key lipolytic bacterium Prevotella sp. R79. Untargeted metabolomics showed marked disruptions in sphingolipid metabolism and linoleic acid oxidation, where the accumulation of cytotoxic oxidized fatty acids (12,13-EpOME) and membrane turnover markers (sphingosine) positively correlated with enriched Bacillota. In summary, under macroscopic acid–base homeostasis, masked ZEN-14G directly impairs ruminal lipid metabolism, alters microbial community structure at the strain level, and perturbs cell membrane lipid turnover strictly within an in vitro system. These findings establish a key mechanistic baseline for masked mycotoxin biotransformation in the rumen, highlighting the necessity for future in vivo feeding trials to fully evaluate their systemic risk profile in ruminants.

[This corrects the article DOI: 10.1016/j.mtbio.2025.102289.].

Thiolated polymers were synthesized and applied for the encapsulation of probiotics. Thiolated modified pectins (LMP-SH1, LMP-SH2, and LMP-SH3) were synthesized with different additions of L-cysteine (0.3, 0.6, and 0.9 M) to low methoxyl pectin (LMP) according to the determination of the free thiol group. FT-IR, NMR, XRD, and SEM were used to characterize and verify the successful modification of thiolated modified pectins. The molecular weight of thiolated modified pectin were reduced with the additions of L-cysteine, demonstrating the more homogeneous conformation of LMP-SH polysaccharide formation compared with LMP. Rheological analysis demonstrated that LMP and LMP-SH1 were viscoelastic fluid like properties, and LMP-SH2 and LMP-SH3 were solid-like gel properties. With a high addition of L-cysteine (LMP-SH3), the LMP-SH hydrogel was rapidly formed at a concentration of 5% (w/v), and its resistance to external strains was limited. Thermal stability was demonstrated for LMP-SH2 and LMP-SH3 at concentrations of 4% and 5% (w/v) over a temperature range of 25-80 degrees C. LMP-SH2 and LMP-SH3 hydrogels were applied to encapsulate the probiotic with high encapsulation efficiency (95.67 +/- 1.22 to 99.54 +/- 0.45%) and desirable protective ability (more than 80% of the survival rate of hydrogel) in the simulated gastrointestinal environment. These results demonstrated LMP-SH could be a good candidate for polysaccharide modification strategy, and the LMP-SH hydrogel could be a good design for pro-biotic encapsulation system.

The discovery of antibiotics saved many lives. Infections were not as deadly a problem for clinicians as they once were. However, due to inappropriate and excessive use of antibiotics, antibiotic resistance has increased dramatically worldwide. Infectious diseases are becoming more challenging to control, and they cause increased morbidity and mortality. Also, a significant risk to human health is posed by infections associated with biofilms. To combat these drug-resistant microorganisms, several novel and alternative strategies have been identified. Bee products such as honey, bee pollen, propolis, royal jelly, bee venom, bee wax, and bee bread have the potential of being used as antimicrobial or antibiofilm agents in various industrial and medical applications. Although these products have some restrictions such as their varying and complex composition, they possess significant potential in the field of medical practices as viable alternatives to antibiotics. They offer a potential solution to the issue of antibiotic resistance. The objective of this review was to offer a comprehensive analysis and evaluation of strategies based on bee products that are currently employed or have been suggested against antimicrobial resistance.

Subcritical water was a promising, clean technique to efficiently pretreat the biomass and further promote the bioethanol conversion. However, the relatively lower removal rate of lignin from biomass after subcritical water pretreatment might be the main reason for the low conversion efficiency of bioethanol. For the purpose of resolving the proposed problem, ethanol was added into subcritical water as an additive to improve pretreatment efficiency in this present study. Response surface methodology based on glucose concentration after enzymatic hydrolysis was adopted to optimized pretreatment process, and the optimum conditions were obtained as 220 degrees C in temperature, 20 min in time, 29.19% in ethanol concentration, and 35.73 (v/w) in liquid-solid ratio. After water-ethanol system pretreatment, the glucose concentration was up to 19.80 +/- 0.38 g/L, which was much higher than that of 9.99 +/- 0.44 g/L of subcritical water pretreatment. Besides, the chemical components, surface morphology, and crystallinity of residues in vital steps were also conducted, indicating that water-ethanol system might be beneficial to improve the pretreatment efficiency. Moreover, the optimal enzymatic hydrolysis conditions of 30 FPU/g (CEL-01), 1 U/g (SPE-007AL), 16% (w/v) loading, and 72 h of time were determined. Meanwhile, based on optimal enzymatic hydrolysis conditions, the ethanol concentration generated by waterethanol system was up to 27.38 +/- 0.47 g/L (SHF) and 29.98 +/- 0.24 g/L (SSSF), which were all much higher than that of subcritical water pretreatment. Besides, ethanol recovery was also investigated, which could be reused in the next pretreatment process. In summary, water-ethanol system was a more effective method for biomass pretreatment to promote bioethanol conversion.

Accumulated evidence supports the beneficial role of inulin in alleviating metabolic dysfunction-associated fatty liver disease (MAFLD) by modulating gut microbiota. However, the underlying mechanisms are not fully understood. Here we used high-fat diet (HFD)-induced laying hen model of MAFLD to investigate the effect of inulin on ameliorating MAFLD and found that the inulin-enriched Megamonas genus was inversely correlated with hepatic steatosis-related parameters. Oral administration of a newly isolated commensal bacterium by culturomics, M. funiformis CML154, to HFD-fed hens and mice ameliorated MAFLD, changed liver gene expression profiles, and increased intestinal propionate concentration. Further evidence demonstrated that the anti-MAFLD effect of M. funiformis CML154 is attributed to propionate-mediated activation of the APN-AMPK-PPARα signaling pathway, thereby inhibiting fatty acid de novo synthesis and promoting β-oxidation. These findings establish the causal relationships among inulin, M. funiformis, and MAFLD, and suggest that M. funiformis CML154 is a probiotic candidate for preventative or therapeutic intervention of MAFLD.

Revealing the assembly and succession of the chicken gut microbiota is critical for a better understanding of its role in chicken physiology and metabolism. However, few studies have examined dynamic changes of absolute chicken gut microbes using the quantitative microbiome profiling (QMP) method. Here, we revealed the developmental trajectory of the broiler chicken gut bacteriome and mycobiome by combining high-throughput sequencing with a microbial load quantification assay. We showed that chicken gut microbiota abundance and diversity reached a plateau at 7 days posthatch (DPH), forming segment-specific community types after 1 DPH. The bacteriome was more impacted by deterministic processes, and the mycobiome was more affected by stochastic processes. We also observed stage-specific microbes in different gut segments, and three microbial occurrence patterns including "colonization," "disappearance," and "core" were defined. The microbial co-occurrence networks were very different among gut segments, with more positive associations than negative associations. Furthermore, we provided links between the absolute changes in chicken gut microbiota and their serum metabolite variations. Time-course untargeted metabolomics revealed six metabolite clusters with different changing patterns of abundance. The foregut microbiota had more connections with chicken serum metabolites, and the gut microbes were closely related to chicken lipid and amino acid metabolism. The present study provided a full landscape of chicken gut microbiota development in a quantitative manner, and the associations between gut microbes and chicken serum metabolites further highlight the impact of gut microbiota in chicken growth and development.

Propolis is a natural resinous substance that is collected by honeybees (Apis mellifera) with promising antibacterial effects. Here, we examined the antibacterial activity of Chinese propolis against Clostridium perfringens, a bacterial pathogen that threatens food safety and causes intestinal erosion. The inhibitory effects of the ethanolic extract of Chinese propolis (CPE) on human-associated C. perfringens strains were determined by using the circle of inhibition, the minimum inhibitory concentrations, and bactericidal concentrations. CPE also induced morphological elongation, bacterial cell wall damage, and intracellular material leakage in C. perfringens. Untargeted HPLC-qTOF-MS-based metabolomics analysis of the bacterial metabolic compounds revealed that propolis triggered glycerophospholipid metabolism, one carbon pool by folate, and d-glutamine and d-glutamate metabolism alterations in C. perfringens. Finally, caffeic acid phenethyl ester was identified as the key active ingredient in CPE. This study suggested the usage of propolis as an alternative to antibiotics in controlling C. perfringens.

Poultry meat and eggs are among the most common sources of animal protein for humans worldwide. The global poultry market was valued at $322.55 billion USD in 2020 and will reach $422.97 billion USD in 2025 at a compound annual growth rate of 7%. Asia Pacific was the largest region in the global poultry market in 2020, contributing to 32% of the total market. In China, 15.57 billion poultry were slaughtered in 2020 with a year-over-year increase of 6.35%. A growing demand for raw poultry and poultry products worldwide has put forward new requirements for sustainable poultry production. Antimicrobials have been widely used in animal farming ever since the addition of low doses of antibiotics to the animal diet was discovered to promote animal growth in the 1950s. It is estimated that in the United States, 70% of antibiotics (24.5 million pounds per year) are used in animals, while only 30% are consumed by humans. The heavy use of antimicrobials for both therapeutic and growth-promoting purposes in farm animals fuels the development and dissemination of antimicrobial resistance among animals, humans, and environments.1Hu Y. Gao G.F. Zhu B. The antibiotic resistome: gene flow in environments, animals and human beings.Front. Med. 2017; 11: 161-168Crossref PubMed Scopus (63) Google Scholar Fortunately, an increasing number of countries have banned the use of antimicrobials as growth promoters in recent years. China banned colistin in 2017 and all antimicrobial growth promoters in 2020. These actions are beneficial for preventing the development of antimicrobial resistance and reducing drug residues in animal foods; however, they pose challenges for maintaining the efficiency and sustainability of food animal production. The basic question of why antimicrobials promote animal growth is still unanswered, which impedes the effectiveness of finding antimicrobial alternatives. However, accumulated evidence has suggested that the growth-promoting effects of antimicrobials were due to their influences on animal gut microbiota. A moderate shift in microbiome composition (limited or no loss of population size) of the animals treated with antimicrobials may result in an optimal microbiota that can change the host physiology and metabolism and reduce intestinal defense, thus enabling the animals to reach their genetic potential.2Cox L.M. Blaser M.J. Antibiotics in early life and obesity.Nat. Rev. Endocrinol. 2015; 11: 182-190Crossref PubMed Scopus (359) Google Scholar Currently, antimicrobial alternatives showing growth-promoting effects, including probiotics, prebiotics, organic acids, enzymes, phytogenics, etc., have all been proven to modulate the gut microbiome. Similar to humans and other animals, the poultry gut is inhabited by a great number of microbes involved in host immune modulation, nutrient metabolism, and pathogen exclusion, etc.3Feng Y. Wang Y. Zhu B. et al.Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes.Commun. Biol. 2021; 4: 1305Crossref PubMed Scopus (15) Google Scholar An optimal and balanced chicken gut microbiome is necessary for a healthy animal and is a prerequisite for better production performance. In addition to using the well-recognized antimicrobial alternatives, it has also been found to be reasonable and feasible to directly manipulate the poultry gut microbiome, e.g., through fecal microbiota transplantation. However, although reconstructing a new microecosystem and/or transferring a desired trait to farm animals by fecal microbiota transplantation can be achieved in laboratory experiments, it is not easy to perform this in practical production processes, especially under modern intensive farming conditions. To overcome the limitations, the construction of artificial bacterial communities, i.e., synthetic microbiomes or communities, has received substantial interest. Using defined microbes from the donor feces to restore the gut ecosystem or transfer an expected phenotype to the receivers guarantees controllability, reproducibility, and safety. Currently, two strategies, "top down" and "bottom up," are proposed and applied in designing synthetic microbiomes (also known as microbiome engineering).4Lawson C.E. Harcombe W.R. Hatzenpichler R. et al.Common principles and best practices for engineering microbiomes.Nat. Rev. Microbiol. 2019; 17: 725-741Crossref PubMed Scopus (216) Google Scholar To date, the effectiveness of designed synthetic microbiomes has been demonstrated with specific goals, ranging from environmental remediation, microbiome-associated disease treatment, immune regulation, and protection and treatment of pathogen infection in plants, humans, and animals. In fact, compound probiotics that have been widely used in poultry production as antimicrobial alternatives can be regarded as a prototype for a synthetic microbiome. However, unlike a simple mixing of different probiotic strains, the synthetic microbiome functions as a whole and features an engineered structure and activity. Given the important role of the gut microbiome in poultry physiology and metabolism, a synthetic microbiome with diverse functions can be expected and designed, including but not limited to the following considerations: (1) reducing antinutritional factors to improve nutrient utilization. For example, insoluble non-starch polysaccharides are a common antinutritional factor in cereal-based poultry feeds, which can be digested using a designed cellulolytic bacterial consortium for fermentation in vitro or as feed additive to function in vivo. (2) Increasing energy supply to improve epithelial absorption and barrier function. Short-chain fatty acid, one of the major products of gut microbes, is an important energy source for gut epithelial cells. A synthetic microbiome with enhanced short-chain fatty acid production is crucial for promoting poultry gut health. (3) Modulating the immune system or inhibiting the colonization of pathogens to reduce infections. Recently, a nine-member synthetic microbial community was designed and demonstrated to effectively promote the maturation of the chicken immune system.5Zenner C. Hitch T.C.A. Riedel T. et al.Early-Life Immune System maturation in chickens using a synthetic community of cultured gut bacteria.mSystems. 2021; 6: e01300-e01320Crossref PubMed Google Scholar (4) Regulating host metabolic signals to prevent metabolic diseases. For instance, in laying hens, fatty liver hemorrhagic syndrome is very similar to the human non-alcoholic fatty liver disease, which can be ameliorated by modulating the gut microbiota and thereby improving the host lipid metabolism. (5) Changing host metabolism to improve the quality and flavor of meat and eggs. Increasing evidence has shown that the quality or flavor of animal products can be regulated by the gut microbiota. It is therefore highly anticipated to use a synthetic microbiome consisting of key gut taxa from better-performing poultries to improve the production traits in receiver animals. In addition to modulating the gut microbiome during poultry rearing, the synthetic microbiome can be applied in other poultry production processes, such as the elimination of mycotoxin contamination in poultry feed; disposal of dead animals (using a designed microbial community to ferment); production of poultry manure compost; and treatment of poultry production sewage. All these possible applications of the synthetic microbiome in poultry production contribute to a sustainable poultry industry (Figure 1). Although fascinating, more efforts are required for designing and effectively applying synthetic microbiomes in poultry production. Challenges and research directions are summarized below. First, the role of gut microbes and mechanisms involved in poultry health and disease is not fully understood. For instance, which microbes regulate growth speed, food intake, and disease resistance in certain poultry individuals and through what mechanisms? How do poultry genetics interact with gut microbes and thus codetermine animal phenotypes? Can the host select specific microbes to colonize and have beneficial effects? What are the keystone taxa (or core microbiome), and how do they interact with other microbes in a balanced poultry gut microbiome to exert beneficial effects on the host? Are there "epidemic probiotics" in different types of poultry? Answering these questions is essential for synthesizing microbial communities with defined functions. Additionally, revealing causal relationships, but not associations, in poultry microbiome studies is highly expected. Second, obtaining pure bacterial cultures and exploring the function of the microbiome at the strain level is key to synthesizing the microbiome. Recently, culturomics, an approach combining high-throughput cultivation (multiple culture conditions) and identification (MALDI-TOF mass spectrometry and 16S rRNA sequencing) of bacteria in a community, has been performed in both human and animal microbiome studies. The culturomic approach enables the culture of hundreds of new microbes that can be utilized as the basic units in the synthetic microbiome. However, in poultry, microbial culturomics is just at the beginning. Large-scale cultivation studies and new microbial culture and identification techniques, e.g., a microfluidic-based cell separation and cultivation method, are continuously needed in poultry-associated microbial communities. Third, a stable synthetic microbiome requires smart design by taking full consideration of the microbial interactions. Different relationships exist among microbial individuals, including mutualism, commensalism, ammensalism, and competition, among others. Cooperative metabolite cross-feeding among microbes prioritizes other interactions in designing synthetic microbiomes. Additionally, when needed, metabolic/genetic engineering and metabolic modeling combined with in silico metabolic flux reconstruction should be fully considered in a well-designed microbiome. Fourth, more efforts should be made with respect to how to use a synthetic microbiome in production practices, especially how to introduce it into animal guts. As gut microbes may have a colonization "priority effect," we suggest an early-life inoculation of the designed consortium, for example through an in ovo injection technique that has been successfully used for administering probiotics in chicken gut. Alternatively, after hatching, a synthetic microbiome can be introduced to the birds through drinking water or be directly gavaged into the crop. Lastly, applying a synthetic microbiome in poultry production is a typical interdisciplinary activity; cooperation among experts in microbiology, animal science, computational biology, and engineering science is highly needed. This work was supported by the Hainan Provincial Natural Science Foundation of China (2021JJLH0084); the National Key Research and Development Program of China (2022YFA1304201); and the 2115 Talent Development Program of China Agricultural University and Chinese Universities Scientific Fund. The authors declare no competing interests.

BACKGROUND:Ginkgo biloba extract (GBE) is evidenced to be effective in the prevention and alleviation of metabolic disorders, including obesity, diabetes and fatty liver disease. However, the role of GBE in alleviating fatty liver hemorrhagic syndrome (FLHS) in laying hens and the underlying mechanisms remain to be elucidated. Here, we investigated the effects of GBE on relieving FLHS with an emphasis on the modulatory role of GBE in chicken gut microbiota.RESULTS:The results showed that GBE treatment ameliorated biochemical blood indicators in high-fat diet (HFD)-induced FLHS laying hen model by decreasing the levels of TG, TC, ALT and ALP. The lipid accumulation and pathological score of liver were also relieved after GBE treatment. Moreover, GBE treatment enhanced the antioxidant activity of liver and serum by increasing GSH, SOD, T-AOC, GSH-PX and reducing MDA, and downregulated the expression of genes related to lipid synthesis (FAS, LXRα, GPAT1, PPARγ and ChREBP1) and inflammatory cytokines (TNF-α, IL-6, TLR4 and NF-κB) in the liver. Microbial profiling analysis revealed that GBE treatment reshaped the HFD-perturbed gut microbiota, particularly elevated the abundance of Megasphaera in the cecum. Meanwhile, targeted metabolomic analysis of SCFAs revealed that GBE treatment significantly promoted the production of total SCFAs, acetate and propionate, which were positively correlated with the GBE-enriched gut microbiota. Finally, we confirmed that the GBE-altered gut microbiota was sufficient to alleviate FLHS by fecal microbiota transplantation (FMT).CONCLUSIONS:We provided evidence that GBE alleviated FLHS in HFD-induced laying hens through reshaping the composition of gut microbiota. Our findings shed light on mechanism underlying the anti-FLHS efficacy of GBE and lay foundations for future use of GBE as additive to prevent and control FLHS in laying hen industry.

ABSTRACTGrowing evidence has shown a close connection between gut microbiota and chicken growth performance; however, the crosstalk between microbes and chicken host remains elusive. Here, we integrated multi-omics approaches, fecal microbiota transplantation, and body weight-associated bacterial consortium to investigate the host-microbiota interactions in different body weight chickens. Microbial profiling analysis showed that uncultured Barnesiellaceae, Lactobacillus, Bacillus, Ruminococcaceae UCG-004, and Ruminococcaceae UCG-014 were highly enriched in the high body weight (HBW) chickens. The combination of Lactobacillus and Bacillus had 95.1% accuracy in discriminating HBW from low body weight chickens. Lipids and lipid-like molecules were found to be more abundant in the HBW chickens, and the differentially expressed cecal genes were enriched in the peroxisome proliferator-activated receptor (PPAR) signaling pathway and calcium signaling pathway. Correlations among the weight-associated genera, gut content metabolites, and gut gene expression were established, and fecal microbiota transplantation from HBW microbiota to newly born chicks increased the chicken antioxidant status, gut sugar transport, and immunity. A total of 67 strains belonging to Lactobacillus and Bacillus were isolated from the HBW chickens by the targeted culturomics method. Among six pairwise combinations of four selected strains, the consortium consisting of Limosilactobacillus reuteri CML393 and Bacillus velezensis CML396 significantly improved the chicken growth performance and gut health and influenced the cecal microbiota, metabolites, and gene expression. Further in vitro and in silico analyses indicated that L. reuteri CML393 and B. velezensis CML396 were less competitive but more cooperative than other pairwise combinations tested.IMPORTANCEThe improvement of chicken growth performance is one of the major concerns for the poultry industry. Gut microbes are increasingly evidenced to be associated with chicken physiology and metabolism, thereby influencing chicken growth and development. Here, through integrated multi-omics analyses, we showed that chickens from the same line differing in their body weight were very different in their gut microbiota structure and host-microbiota crosstalk; microbes in high body weight (HBW) chickens contributed to chicken growth by regulating the gut function and homeostasis. We also verified that a specific bacterial consortium consisting of isolates from the HBW chickens has the potential to be used as chicken growth promoters. These findings provide new insights into the potential links between gut microbiota and chicken phenotypes, shedding light on future manipulation of chicken gut microbiota to improve chicken growth performance.

Background Alginate oligosaccharide (AOS) holds great potential as a novel feed supplement in farm animals. However, the effects of AOS on chicken health and the underlying mechanisms are not fully understood. This study aimed to optimize the enzymatic preparation of AOS by using bacterial alginate lyases expressed in yeast, investigate the effects of the prepared AOS on the growth performance and gut health of broiler chickens, and reveal the underlying mechanisms. Results Five alginate lyases from bacteria were cloned into Pichia pastoris GS115 and the alginate lyase PDE9 was expressed at relatively high yield, activity and stability in P. pastoris . Animal trials were carried out using 320 1-day-old male Arbor Acres broilers (four groups; 8 replicates/group × 10 chicks/replicate) receiving either a basal diet or the same diet supplemented with 100, 200 and 400 mg/kg PDE9-prepared AOS for 42 d. The results showed that dietary supplementation of 200 mg/kg AOS displayed the highest activity in promoting the birds’ ADG and ADFI ( P < 0.05). AOS ameliorated the intestinal morphology, absorption function and barrier function, as indicated by the enhanced ( P < 0.05) intestinal villus height, maltase activity, and the expression of PEPT , SGLT1 , ZNT1 , and occludin. AOS also increased serum insulin-like growth factor-1, ghrelin ( P < 0.05), and growth hormone ( P < 0.1). Moreover, the concentrations of acetate, isobutyrate, isovalerate, valerate, and total SCFAs in cecum of birds fed AOS were significantly higher than the control birds ( P < 0.05). Metagenomic analysis indicated that AOS modulated the chicken gut microbiota structure, function, and microbial interactions and promoted the growth of SCFAs-producing bacteria, for example, Dorea sp. 002160985; SCFAs, especially acetate, were found positively correlated with the chicken growth performance and growth-related hormone signals ( P < 0.05). We further verified that AOS can be utilized by Dorea sp. to grow and to produce acetate in vitro. Conclusions We demonstrated that the enzymatically produced AOS effectively promoted broiler chicken growth performance by modulating the chicken gut microbiota structure and function. For the first time, we established the connections among AOS, chicken gut microbiota/SCFAs, growth hormone signals and chicken growth performance. Graphical Abstract

The gut microbiota makes important contributions to host immune system development and resistance to pathogen infections, especially during early life. However, studies addressing the immunomodulatory functions of gut microbial individuals or populations are limited. In this study, we explore the systemic impact of the ileal microbiota on immune cell development and function of chickens and identify the members of the microbiota involved in immune system modulation. We initially used a time-series design with six time points to prove that ileal microbiota at different succession stages is intimately connected to immune cell maturation. Antibiotics perturbed the microbiota succession and negatively affected immune development, whereas early exposure to the ileal commensal microbiota from more mature birds promoted immune cell development and facilitated pathogen elimination after Salmonella Typhimurium infection, illustrating that early colonization of gut microbiota is an important driver of immune development. Five bacterial strains, Blautia coccoides , Bacteroides xylanisolvens , Fournierella sp002159185, Romboutsia lituseburensis , and Megamonas funiformis , which are closely related to the immune system development of broiler chickens, were then screened out and validated for their immunomodulatory properties. Our results provide insight into poultry immune system–microbiota interactions and also establish a foundation for targeted immunological interventions aiming to combat infectious diseases and promote poultry health and production.

Maintaining animal gut health through modulating the gut microbiota is a constant need when antibiotics are not used in animal feed during the food animal production process. Prebiotics is regarded as one of the most promising antibiotic alternatives for such purpose. As an attractive prebiotic, the role and mechanisms of neoagarooligosaccharides (NAOS) in promoting animal growth and gut health have not been elucidated. In this study, we first cloned and expressed marine bacterial β-agarase in yeast to optimize the NAOS preparation and then investigated the role and the underlying mechanisms of the prepared NAOS in improving chicken gut health and function. The marine bacterial β-agarase PDE13B was expressed in Pichia pastoris GS115 and generated even-numbered NAOS. Dietary the prepared NAOS promoted chicken growth and improved intestinal morphology, its barrier, and digestion capabilities, and absorption function. Metagenomic analysis indicated that NAOS modulated the chicken gut microbiota structure and function, and microbial interactions, and promoted the growth of spermidine-producing bacteria especially Faecalibacterium. Through integration of gut metagenome, gut content metabolome, and gut tissue transcriptome, we established connections among NAOS, gut microbes, spermidine, and chicken gut gene expression. The spermidine regulation of genes related to autophagy, immunity, and inflammation was further confirmed in chicken embryo intestinal epithelium cells. We also verified that NAOS can be utilized by Faecalibacterium prausnitzii to grow and produce spermidine in in vitro experiments. Collectively, we provide a systematic investigation of the role of NAOS in regulating gut health and demonstrate the microbial spermidine-mediated mechanism involved in prebiotic effects of NAOS, which lays foundation for future use of NAOS as a new antibiotic alternative in animal production.

Oregano (Origanum vulgare L.) is a well-known traditional medicine and a cooking spice. Recent practice has also applied the essential oil from oregano (OEO) in poultry due to its great potential for an antibiotic alternative. Our objective was to evaluate the potential effects of OEO (with carvacrol and thymol as the main active ingredient) on preventing necrotic enteritis (NE) caused by Clostridium perfringens (Cp) in chickens. In the feeding trial, a total of 450 one-day-old commercial Arbor Acres broilers were randomly assigned in 5 experimental groups during a 26-day production period (d19 to d 26 was the Cp challenge stage), and each group consisted of 6 replicate pens (15 birds each pen). All treatments were: basal diet (control group); basal diet and Cp challenge (model group); Cp challenge and 10 mg/kg enramycin (positive control group); Cp challenge and 200 mg/kg OEO product (OEO low dosage group, OEOL); Cp challenge and 300 mg/kg OEO product (OEO high dosage group, OEOH). OEO feed supplement at both dosages had significant effects on increasing the body weight gain (BWG) and reversing the dropped feed intake (FI) induced by Cp challenge. Histopathological changes in the ileums of broiler chickens with NE induced by Cp were alleviated by OEO, which was mutually confirmed by the intestinal lesion scores. Dosage did not influence the protective effect of OEO on intestinal lesion scores. Furthermore, OEO was found to have limited effects on tight junction-related gene expressions (Occludin and ZO-1). The broilers of the OEOL and OEOH groups significantly decreased the expression of TNF-α mRNA in the ileum and only the OEOH group was found to inhibit the IFN-γ expression of IFN- induced by Cp challenge. Finally, despite the fact that in vitro antibacterial effects by OEO were observed, considering its high minimum inhibitory concentration (MIC) value, we inferred that the protective effects by OEO against Cp challenge were not attributable to its direct antibacterial effects. We proposed OEO as a promising substitute for antibiotics against NE induced by Cp during poultry production.

Intestinal diseases cause huge economic losses in farm animals, and the gut health of livestock and poultry is of great significance for livestock and poultry breeding. The traditional treatment of livestock and poultry involved large-scale use of antibiotics and led to antibiotic abuse. The replacement of antibiotics is an industrial demand, and plant polyphenols, as one of the non-toxic side effects and residues of antibiotics, have wide applications in livestock and poultry production and diseases. As a non-traditional nutrient with many advantages, plant polyphenols have great potential and great research value. This article summarizes research advances on the beneficial effects of plant polyphenols on intestinal health in farm animals from three aspects: the application of plant polyphenols as antibiotic substitutes in livestock and poultry production, the protective effects of plant polyphenols on the intestinal tract of livestock and poultry, and the protective mechanism.

Clostridium perfringens is associated with a variety of diseases in both humans and animals. Recent advances in genomic sequencing make it timely to re-visit this important pathogen. Although the genome sequence of C. perfringens was first determined in 2002, large-scale comparative genomics with isolates of different origins is still lacking. In this study, we used whole-genome sequencing of 45 C . perfringens isolates with isolation time spanning an 80‐year period and performed comparative analysis of 173 genomes from worldwide strains. We also conducted phylogenetic lineage analysis and introduced an openness index (OI) to evaluate the openness of bacterial genomes. We classified all these genomes into five lineages and hypothesized that the origin of C. perfringens dates back to ~80 000 years ago. We showed that the pangenome of the 173 C . perfringens strains contained a total of 26 954 genes, while the core genome comprised 1020 genes, accounting for about a third of the genome of each isolate. We demonstrated that C. perfringens had the highest OI compared with 51 other bacterial species. Intact prophage sequences were found in nearly 70.0 % of C. perfringens genomes, while CRISPR sequences were found only in ~40.0 %. Plasmids were prevalent in C. perfringens isolates, and half of the virulence genes and antibiotic resistance genes (ARGs) identified in all the isolates could be found in plasmids. ARG-sharing network analysis showed that C. perfringens shared its 11 ARGs with 55 different bacterial species, and a high frequency of ARG transfer may have occurred between C. perfringens and species in the genera Streptococcus and Staphylococcus . Correlation analysis showed that the ARG number in C. perfringens strains increased with time, while the virulence gene number was relative stable. Our results, taken together with previous studies, revealed the high genome openness and genetic diversity of C. perfringens and provide a comprehensive view of the phylogeny, genomic features, virulence gene and ARG profiles of worldwide strains.

Galangin is a natural flavonoid that has been reported to provide substantial health benefits. Nevertheless, little is known about the potential effects of galangin against inflammatory bowel diseases. Here, an in vivo study was performed to investigate the preventive effects of galangin against dextran sulphate sodium (DSS)-induced acute murine colitis, which mimics the symptoms of human ulcerative colitis (UC). Pre-treatment with galangin (15 mg/kg, p.o.) resulted in a significant decreased in the macroscopic signs of DSS-induced colitic symptoms, including a decreased disease activity index, prevention of the colon length shortening, and alleviation of the pathological changes occurring in the colon. Colonic pro-inflammatory mediators, including tumor necrosis factor-alpha, interleukin (IL)-1 beta, and IL-6, as well as myeloperoxidase activities were decreased following galangin pre-treatment when compared with the DSS control group. Moreover, galangin pre-treatment significantly increased the expressions of autophagy-related proteins and promoted the formation of autophagosome in the colon. Galangin pre-treatment increased the diversity of the gut microbiota, and this was accompanied by increased levels of short-chain fatty acids. These observed changes could involve the modulating effects conferred by galangin in relation to some specific bacteria populations, including the recovery of Lactobacillus spp., and increased Butyricimonas spp. Overall, these results support the use of galangin in the prevention of UC.