The digestive and reproductive tract microbiotas and their association with body weight in laying hens

Influence of Body Weight at the End of the Brooding Period on the Productive Performance in Hyline Brown Laying Hens from 6 to 72 Weeks of Age

This research aimed to assess body weight (BW) at the end of the brooding period in affecting Hyline Brown laying hens aged 6 to 72 wks from the aspects of growth performance, egg quality, sexual maturity, and productive performance. Pullets (6 wk old, n = 640) were sorted into two groups according to BW: normal (460.75 ± 10.82 g) and light (347.96 ± 6.27 g, 75.52% of normal weight), with eight replicates of 40 pullets each. All the hens, when reaching 6-72 wks in age, took the same diets by stages ad libitum. The heavier BW in the normal weight group (NWG) at 6 wks of age compared to lighter weight group (LWG) birds continued until 22 wks (p < 0.05). Similarly, a smaller coefficient of variation (CV) for BW of chicks in the LWG was detected at 19 (p < 0.01), 20 (p < 0.01), and 21 (p < 0.05) wks of age compared with that in the NWG. The body slope length and the shank circumference of pullets in the LWG were smaller than in the NWG at the age of 15 wks (p < 0.01), but the difference gradually disappeared by 20 wks of age (p > 0.05). The LWG presented raised ages of hens when producing the first egg and 5% eggs (p < 0.01), while the CV for the age at first egg decreased, compared with the CV in the NWG (p < 0.05). The total egg number (p < 0.05), laying rate (p < 0.05), and egg mass (p < 0.01) of laying hens in the LWG decreased at the age of 18-72 wks, and the CV for individual egg numbers (p < 0.05) increased compared with the CV in the NWG. Compared with the normal weight hens, the proportion of lighter weight hens laying more than 250 eggs at the age of 18-72 wks was significantly reduced (p < 0.05, 69.52% vs. 87.38%), while the proportion of hens laying less than 200 eggs was significantly increased (p < 0.05, 24.97% vs. 3.76%). In summary, BW by the end of the brooding period can be a good indicator reflecting individual differences among laying hens and may serve as an important phenotypic indicator for evaluating laying performance and early elimination of unqualified laying hens in layer production. Therefore, it is recommended that pullets weighing 25% or more below the normal flock weight at the end of the brooding period should be culled at this time.

Effects of Embryonic Thermal Manipulation on Body Performance and Cecum Microbiome in Broiler Chickens Following a Post-Hatch Lipopolysaccharide Challenge

Thermal manipulation (TM) during embryogenesis has emerged as a promising strategy to enhance post-hatch performance and improve resilience to environmental and bacterial stress, which offers a potential alternative to reduce the reliance on antibiotic growth promoters (AGPs) in broiler production. This study investigated TM's ability to modulate broilers' cecal microbiota and enhance resilience to lipopolysaccharide (LPS)-induced stress. Eggs in the control group (CON) were incubated at 37.8 °C and 56% relative humidity (RH), while TM eggs were exposed to 39 °C and 65% RH for 18 h daily from embryonic days 10-18. Post-hatch, the LPS subgroups (LPS-CON, LPS-TM) received intraperitoneal LPS injections, and body weight (BW) and temperature (BT) were monitored. Cecal samples were collected for microbiome sequencing. Alpha diversity showed no differences (p > 0.05), but beta diversity revealed differences between groups (PERMANOVA, p < 0.05). Firmicutes and Bacteroidota dominated the microbiota at the phylum level. Oscillospirales were enriched in the TM groups (p < 0.001) and Lactobacillales were increased in the LPS-CON group (p < 0.019). LPS reduced BT in the CON group (p < 0.01), but LPS-TM birds bypassed hypothermia. LPS significantly reduced BW (p < 0.001), while TM had no significant effect. These findings demonstrate TM's enduring influence on gut microbiota and stress resilience, highlighting its potential to reduce antibiotic reliance and mitigate antimicrobial resistance (AMR) in poultry production.

Gut Metagenome Reveals the Microbiome Signatures in Tibetan and Black Pigs

The harsh conditions of the Qinghai-Tibet Plateau pose significant physiological challenges to local fauna, often resulting in gastrointestinal disorders. However, Tibetan pigs have exhibited remarkable adaptability to the high-altitude stress of the Tibetan Plateau, a phenomenon that remains not fully understood in terms of their gastrointestinal microbiota. This study collected 57 gastrointestinal tract samples from Tibetan pigs (n = 6) and plain black pigs (n = 6) with comparable genetic backgrounds. Samples from the stomach, jejunum, cecum, colon, and rectum, underwent comprehensive metagenomic analysis to elucidate the gut microbiota-related adaptive mechanisms in Tibetan pigs to the extreme high-altitude environment. A predominance of Pseudomonadota was observed within gut microbiome of Tibetan pigs. Significant differences in the microbial composition were also identified across the tested gastrointestinal segments, with 18 genera and 141 species exhibiting differential abundance. Genera such as Bifidobacterium, Megasphaera, Fusobacterium, and Mitsuokella were significantly more abundant in Tibetan pigs than in their lowland counterparts, suggesting specialized adaptations. Network analysis found greater complexity and modularity in the microbiota of Tibetan pigs compared to black pigs, indicating enhanced ecological stability and adaptability. Functional analysis revealed that the Tibetan pig microbiota was particularly enriched with bacterial species involved in metabolic pathways for propionate and butyrate, key short-chain fatty acids that support energy provision under low-oxygen conditions. The enzymatic profiles of Tibetan pigs, characterized by elevated levels of 4-hydroxybutyrate dehydrogenase and glutaconyl-CoA decarboxylase, highlighted a robust fatty acid metabolism and enhanced tricarboxylic acid cycle activity. In contrast, the gut microbiome of plain black pigs showed a reliance on the succinate pathway, with a reduced butyrate metabolism and lower metabolic flexibility. Taken together, these results demonstrate the crucial role of the gastrointestinal microbiota in the adaptation of Tibetan pigs to high-altitude environments by optimizing carbohydrate metabolism and short-chain fatty acid production for efficient energy utilization. This study not only highlights the metabolic benefits conferred by the gut microbiota of Tibetan pigs in extreme environments, but also advances our understanding of the adaptive gastrointestinal mechanisms in plateau-dwelling animals. These insights lay the foundation for exploring metabolic interventions to support health and performance in high-altitude conditions.

Gut bacterial and fungal communities of François' langur (Trachypithecus francoisi) changed coordinate to different seasons

Introduction

François' langur (Trachypithecus francoisi), an endangered primate endemic to limestone forests in Vietnam and China, relies on gut microbiota to maintain gastrointestinal stability and adapt to dietary shifts. While gut microbial communities are dynamic and sensitive to seasonal and resource variations, their specific responses in François' langurs remain poorly characterized. This study investigates seasonal variations in the composition and diversity of gut bacterial and fungal communities in this species to enhance understanding of its ecological adaptations.

Methods

Fresh fecal samples from 22 François' langurs in Mayanghe National Nature Reserve, China, were collected across four seasons. Bacterial and fungal communities were analyzed using high-throughput sequencing to assess taxonomic composition and α-diversity. Statistical comparisons were conducted to evaluate seasonal differences at phylum and genus levels.

Results

Significant seasonal shifts occurred in both bacterial and fungal communities. Bacterial α-diversity peaked in warmer seasons, whereas fungal diversity was higher in colder months. At the genus level, Akkermansia (1.3% relative abundance in summer), a mucin-degrading bacterium linked to gut health, dominated warmer seasons. In contrast, the fungal genus Cercophora, associated with plant biomass degradation, was enriched during colder seasons. Seasonal factors strongly influenced microbial structure, with distinct community assemblages observed across all seasons.

Discussion

The inverse diversity patterns of bacterial and fungal communities suggest complementary roles in nutrient extraction under seasonal dietary constraints. Akkermansia's summer prevalence may reflect enhanced mucin utilization during fruit-rich periods, while Cercophora's cold-season dominance likely aids cellulose breakdown in leaf-heavy diets. These dynamics highlight the microbiota's role in optimizing energy harvest from seasonally variable diets. By elucidating microbial seasonal plasticity, this study provides critical insights for developing conservation strategies tailored to the nutritional ecology of François' langurs.

Probiotics improve eggshell quality via regulating microbial composition in the uterine and cecum

Probiotics benefit the health and production performance of chickens, but their impact on egg and eggshell quality, particularly in the later stage, remains unclear. Here, 1-day-old Tianfu green shell-laying hens were fed either non-probiotics feed (n = 180) or feed supplemented with 100 mg / kg probiotics (n = 180). 16S rDNA sequencing indicated that dietary probiotics decreased the distribution of uterine p_Firmicutes, g_Fusobacterium, and s_Fusobacterium_unclassified, while increased p_Proteobacteria, g_Ralstonia, and s_Ralstonia_unclassified. PICRUSt2 and Bug Base analysis revealed enrichment in fatty acid metabolism, thiamine metabolism, vitamin B6 metabolism pathways and increased relative abundance of Proteobacteria, Firmicutes, Bacteroidetes. With LDA > 4.5, 35 and 25 marker bacterial taxa were identified in the uterus and cecum, respectively. Probiotics significantly increased uterine villi length and width, and the expressions of ATP2B2,SLC26A9,TF,OC-17,OCX-32, and OVAL in the uterus at the early and peak laying stage. Meantime, probiotics improved egg quality, pore density of eggshell barrier layer, and levels of Ca2+, Na+, and Mg2+, whereas dropped levels of P3-, S2- and K+ in eggshell. In serum, Ca2+, K+, Na+ had a response to dietary probiotics at different laying stages, except Cl-. Furthermore, the changes of these phenotypes are closely related to the microbial structure of the uterus and cecum. Overall, the data suggest that dietary probiotics improved uterine and cecal microbiota, optimized egg quality, eggshell quality, uterus development, and regulated mineralization gene expression and ion content in serum and eggshell, thereby improving productivity of laying hens. These results provide reference for the application of probiotics in the laying industry.

How does gut microbiota affect the vaginitis axis? The mediating role of plasma metabolites

Vaginitis is the most common problem afflicting women of childbearing age. However, the underlying etiological factors remain poorly understood, leading to recurrent vaginitis and constraining clinical management. Here, we explored whether the gut microbiota influences the risk of vaginitis by performing a two-sample Mendelian randomization analysis using the largest genome-wide association studies to date. Four gut taxa in genus levels were identified related to vaginitis: Candidatus Soleaferrea (inverse-variance weighted [IVW] odds ratio [OR] = 2.20, P = 0.026), Dialister (IVW OR = 2.62, P = 0.029), Lachnospiraceae UCG-008 (IVW OR = 0.41, P = 0.0067), and Ruminiclostridium 5 (IVW OR = 0.080, P = 1.42 × 10-5). We further explored the mediation effect of the plasma metabolites by two-step Mendelian randomization (MR) and multivariable MR. The findings indicated that 3-phosphoglycerate and lysophosphatidylcholine antagonistically act against the two identified risk factors (Candidatus Soleaferrea and Dialister, respectively) of vaginitis, thus appearing to confer protective effects against vaginitis. On the contrary, the elevation of arachidonate/pyruvate ratio and reduction in palmitate/myristate ratio mediated the protective effects of Lachnospiraceae UCG-008 against vaginitis. These findings support a potential causal role for gut microbiota in the development of vaginitis, thereby providing potential strategies for its prevention and intervention.IMPORTANCEVaginitis is the most common problem afflicting women of childbearing age. However, the underlying etiological factors remain poorly understood, leading to recurrent vaginitis and constraining clinical management. Besides, the human gut and vagina are important organs that are both colonized by thousands of microorganisms impacting human physiology and health. Whether there is an interplay between the microecosystems is intriguing and unclear. This study evaluated the potential causal relationship between the gut microbiota and vaginitis and suggested that specific types of gut microbiota may be the potential risk or protective factors of vaginitis mediated or suppressed by certain plasma metabolites. These findings provide treatment insights for vaginitis.

Research Note: Correlation between the reproductive tract microbiota and speckled eggs in laying hens

The microbiomes of the reproductive tract play a crucial role in the egg production and quality and reproductive health of laying hens. Speckled eggs are characterized by shells with brown spots of varying sizes and commonly produced by brown-shelled laying hens. Speckles reduce the economic value of eggs. However, the relationship between oviduct and cloacal microbiomes and the presence of speckled eggs in laying hens remains unclear. In this study, we collected samples from the reproductive tracts (uterus, vagina, and cloaca) of hens laying speckled eggs and those laying normal eggs and compared their microbial structures and relative abundances through 16S rRNA sequencing. We found that the microbial community structure in the reproductive tracts of the hens laying speckled eggs was similar to that in the reproductive tracts of the hens laying normal eggs; however, the relative abundances of Clostridium in the uterus and Turicibacter and Gallibacterium in the vagina of the hens from the speckled group (7.27%, 6.83% and 0.10%, respectively) were significantly higher than those in the normal group (2.00%, 0% and 0%, respectively [P < 0.05]). Additionally, 8, 24, and 11 bacterial taxa in the uterus, vagina, and cloaca were different between the groups of hens laying speckled and normal eggs. At the same time, Clostridium in the uterus may be associated with eggshell speckles. However, further investigations are necessary to understand the functions of these microbiota in the reproductive tracts of laying hens. This study provides novel insights into methods for reducing the occurrence of speckled eggs in laying hens.

Yacon (Smallanthus sonchifolius) root extracts affect laying performance, egg quality, serum biochemical parameters and intestinal microbiota in hens

OBJECTIVE

The objective of this study was to investigate the influence of yacon root extracts (YREs) on productive performance and health of laying hens.

METHODS

Six hundred 30-week-old Xiaoshan Chicken layers were divided into 5 groups, control group, antibiotic positive control group, and 3 YREs treatment groups. In a 9-wk feeding experiment, at the end of wk 3, 6, and 9, twenty eggs were collected from each replicate to measure egg qualities. At the end of wk 9, three hen serum samples, and 5 hen cecal content samples were collected from each replicate.

RESULTS

Compared to the control group, 0.8%, 1.6%, and 2.4% YREs treatments could increase hens' daily feed intake, and YREs supplementation affected daily feed intake in linear manner. YREs did not change egg size, but 0.8% and 2.4% YREs changed egg shape by decreasing the egg shape index and sphericity, and 0.8% YREs tended to improve the eggshell breaking strength. Diet supplemented with 1.6% YREs might decrease yolk color grade but optimize the pH of thick egg white in fresh egg; moreover, 1.6% and 2.4% YREs might be helpful for eggs to inhibit water loss during storage, and YREs supplementation affected water loss rate in linear manner. 2.4% YREs could decrease the serum lactate dehydrogenases (LDH) level, and YREs supplemental levels linearly affected serum LDH content. Finally, YREs could enrich the diversity of intestinal microbiota of hens fed with 0.8% and be beneficial for the relative abundance of phylum Bacteroidota and Halobacterota; 2.4% YREs might increase the abundance of phylum Actinobacteriota and genus Bifidobacterium, while decrease genus Bacteroides; YREs supplemental levels affected the abundance of phylum Actinobacteriota, and genera Bifidobacterium and Bacteroides in linear manner.

CONCLUSION

Dietary supplementation with YREs could affect egg quality, protect the health of organs and exhibit prebiotic activity.

Metagenomic profiling uncovers microbiota and antibiotic resistance patterns across human, chicken, pig fecal, and soil environments

The ongoing and progressive evolution of antibiotic resistance presents escalating challenges for the clinical management and prevention of bacterial infections. Understanding the makeup of resistance genomes and accurately quantifying the current abundance of antibiotic resistance genes (ARGs) are crucial for assessing the threat of antimicrobial resistance (AMR) to public health. This comprehensive study investigated the distribution and diversity of bacterial community composition, ARGs, and virulence factors (VFs) across human, chicken, pig fecal, and soil microbiomes in various provinces of China. As a result, multidrug resistance was identified across all samples. Core ARGs primarily related to multidrug, MLS (Macrolides-Lincosamide-Streptogramins), and tetracycline resistance were characterized. A significant correlation between ARGs and bacterial taxa was observed, especially in soil samples. Probiotic strains such as Lactobacillus harbored ARGs, potentially contributing to the dissemination of antibiotic resistance. We screened subsets of ARGs from samples from different sources as indicators to assess the level of ARGs contamination in samples, with high accuracy. These results underline the complex relationship between microbial communities, resistance mechanisms, and environmental factors, emphasizing the importance of continued research and monitoring to better understand these dynamics.

Are there consistent effects of gut microbiota composition on performance, productivity and condition in poultry?

Microbiome of the gastrointestinal tract (GIT) has been identified as one of the crucial factors influencing the health and condition of domestic animals. The global poultry industry faces the challenge of understanding the complex relationship between gut microbiota composition and performance-related traits in birds. Considerable variation exists in the results of correlational studies using either 16S rRNA profiling or metagenomics to identify bacterial taxa associated with performance, productivity, or condition in poultry (e.g., body weight, growth rate, feeding efficiency, or egg yield). In this review, we survey the existing reports, discuss variation in research approaches, and identify bacterial taxa consistently linked to improved or deteriorated performance across individual poultry-focused studies. Our survey revealed high methodological heterogeneity, which was in contrast with vastly uniform focus of the research mainly on the domestic chicken (Gallus gallus) as a model. We also show that the bacterial taxa most frequently used in manipulative experiments and commercial probiotics intended for use in poultry (e.g., species of Lactobacillus, Bacillus, Enterococcus, or Bifidobacterium) do not overlap with the bacteria consistently correlated with their improved performance (Candidatus Arthromitus, Methanobrevibacter). Our conclusions urge for increased methodological standardization of the veterinary research in this field. We highlight the need to bridge the gap between correlational results and experimental applications in animal science. To better understand causality in the observed relationships, future research should involve a broader range of host species that includes both agricultural and wild models, as well as a broader range of age groups.

Dynamic Changes in Intestinal Gene Expression and Microbiota across Chicken Egg-Laying Stages

Eggs are a vital dietary component for humans, and it is beneficial to increase egg production to support poultry farming. Initially, the egg production rate rises rapidly with young hens until it reaches its peak, and then it declines gradually. By extending the duration of peak egg production, the hens' performance can be enhanced significantly. Previous studies found dynamic changes in gut microbiota during egg-laying, and several species of microbiota isolated from the chicken gut improved egg-laying performance. However, the interaction between microbes and host gene expression is still unclear. This study provides a more comprehensive understanding of chicken egg-laying by examining dynamic alterations in the microbiota of the entire intestinal tract (i.e., duodenum, jejunum, and ileum) and gene expression. The microbial community in the intestine underwent significant changes during different egg-laying periods (i.e., pre-, peak-, and late-laying periods). Metagenomic functional analysis showed that the relative abundance of biosynthesis of amino acids, secondary metabolites, and cofactors decreased significantly in the duodenum, jejunum, and ileum of aging hens. The relative levels of aldosterone, GnRH, insulin, growth hormone, and other hormone-related pathways increased dramatically in the intestinal microbiota during egg-laying, but only in the microbiota located in the duodenum and ileum. Transcriptome analysis suggested that genes associated with various transport processes were upregulated consistently in the small intestine during egg-laying; genes involved in the development of intestinal structure were down-regulated; and genes involved in response to DNA damage and stress were consistent with changes in laying rate. The abundance of Lactobacillus was related to the expression of ANGPTRL1, ANGPTRL2, ANGPT1L, and NOXO1 in the duodenum; Muricomes was correlated significantly with NFKBIZ, LYG2, and IRG1L expression in the jejunum; and Campylobacter was correlated positively with the expression of KMT2A and USF3 in the ileum. These results indicated that the intestinal microbiota and host gene expression may influence egg production jointly.

Host genetics drives differences in cecal microbiota composition and immune traits of laying hens raised in the same environment

Vaccination is one of the most effective strategies for preventing infectious diseases but individual vaccine responses are highly heterogeneous. Host genetics and gut microbiota composition are 2 likely drivers of this heterogeneity. We studied 94 animals belonging to 4 lines of laying hens: a White Leghorn experimental line genetically selected for a high antibody response against the Newcastle Disease Virus (NDV) vaccine (ND3) and its unselected control line (CTR), and 2 commercial lines (White Leghorn [LEG] and Rhode Island Red [RIR]). Animals were reared in the same conditions from hatching to 42 d of age, and animals from different genetic lines were mixed. Animals were vaccinated at 22 d of age and their humoral vaccine response against NDV was assessed by hemagglutination inhibition assay and ELISA from blood samples collected at 15, 19, and 21 d after vaccination. The immune parameters studied were the 3 immunoglobulins subtypes A, M, and Y and the blood cell composition was assessed by flow cytometry. The composition of the cecal microbiota was assessed at the end of the experiment by analyzing amplified 16S rRNA gene sequences to obtain amplicon sequence variants (ASV). The 4 lines showed significantly different levels of NDV vaccine response at the 3 measured points, with, logically, a higher response of the genetically selected ND3 line, and intermediate and low responses for the unselected CTR control line and for the 2 commercial lines, respectively. The ND3 line displayed also a higher proportion of immunoglobulins (IgA, IgM, and IgY). The RIR line showed the most different blood cell composition. The 4 lines showed significantly different microbiota characteristics: composition, abundances at all taxonomic levels, and correlations between genera and vaccine response. The tested genetic lines differ for immune parameters and gut microbiota composition and functions. These phenotypic differences can be attributed to genetic differences between lines. Causal relationships between both types of parameters are discussed and will be investigated in further studies.

Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens

BACKGROUND

The gut microbiota plays an essential role in maintaining gut homeostasis and improving performance, with the composition of microbial communities visibly differing across different laying stages in hens and significantly correlating with egg production. To gain further insights into the association between microbial community characteristics and laying periods in Hy-Line variety brown and Isa brown laying hens, we conducted a 16S rRNA amplicon sequencing survey.

RESULTS

Our result revealed the diversity of bacteria in the early laying period was commonly higher than peak, and in Hy-Line variety brown laying hens were generally higher than Isa brown. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) revealed that the structure and composition of the gut microbiota of laying hens exhibited significant differences among different groups. Phylum Firmicutes, Bacteroidota, Proteobacteria, and Fusobacteriota were found that dominant in the host's feces. Therein, the abundance of Fusobacteriota was higher in the peak period than in the early period, while the abundance of Cyanobacteria in the early period was higher in two breeds of hens. Furthermore, random forest based on machine learning showed that there were several distinctly abundant genera, which can be used as potential biomarkers to differentiate the different groups of laying periods and breeds. In addition, the prediction of biological function indicated the existing discrepancy in microbial function among the microbiota of four groups.

CONCLUSIONS

Our findings offer new insights into the bacterial diversity and intestinal flora composition of different strains of laying hens during various laying periods, contributing significantly to the improvement of production performance and the prevention of chicken diseases.

Rumen and Fecal Microbiota Characteristics of Qinchuan Cattle with Divergent Residual Feed Intake

Residual feed intake (RFI) is one of the indicators of feed efficiency. To investigate the microbial characteristics and differences in the gastrointestinal tract of beef cattle with different RFI, a metagenome methodology was used to explore the characteristics of the rumen and fecal microbiota in 10 Qinchuan cattle (five in each of the extremely high and extremely low RFI groups). The results of taxonomic annotation revealed that Bacteroidetes and Firmicutes were the most dominant phyla in rumen and feces. Prevotella was identified as a potential biomarker in the rumen of the LRFI group by the LEfSe method, while Turicibacter and Prevotella might be potential biomarkers of the HRFI and LRFI group in feces, respectively. Functional annotation revealed that the microbiota in the rumen of the HRFI group had a greater ability to utilize dietary polysaccharides and dietary protein. Association analysis of rumen microbes (genus level) with host genes revealed that microbiota including Prevotella, Paraprevotella, Treponema, Oscillibacter, and Muribaculum, were significantly associated with differentially expressed genes regulating RFI. This study discovered variances in the microbial composition of rumen and feces of beef cattle with different RFIs, demonstrating that differences in microbes may play a critical role in regulating the bovine divergent RFI phenotype variations.

The active core microbiota of two high-yielding laying hen breeds fed with different levels of calcium and phosphorus

The nutrient availability and supplementation of dietary phosphorus (P) and calcium (Ca) in avian feed, especially in laying hens, plays a vital role in phytase degradation and mineral utilization during the laying phase. The required concentration of P and Ca peaks during the laying phase, and the direct interaction between Ca and P concentration shrinks the availability of both supplements in the feed. Our goal was to characterize the active microbiota of the entire gastrointestinal tract (GIT) (crop, gizzard, duodenum, ileum, caeca), including digesta- and mucosa-associated communities of two contrasting high-yielding breeds of laying hens (Lohmann Brown Classic, LB; Lohmann LSL-Classic, LSL) under different P and Ca supplementation levels. Statistical significances were observed for breed, GIT section, Ca, and the interaction of GIT section x breed, P x Ca, Ca x breed and P x Ca x breed (p &lt; 0.05). A core microbiota of five species was detected in more than 97% of all samples. They were represented by an uncl. Lactobacillus (average relative abundance (av. abu.) 12.1%), Lactobacillus helveticus (av. abu. 10.8%), Megamonas funiformis (av. abu. 6.8%), Ligilactobacillus salivarius (av. abu. 4.5%), and an uncl. Fusicatenibacter (av. abu. 1.1%). Our findings indicated that Ca and P supplementation levels 20% below the recommendation have a minor effect on the microbiota compared to the strong impact of the bird’s genetic background. Moreover, a core active microbiota across the GIT of two high-yielding laying hen breeds was revealed for the first time.

Dynamic Changes in the Gut Microbial Community and Function during Broiler Growth

During the entire growth process, gut microbiota continues to change and has a certain impact on the performance of broilers. Here, we used 16S rRNA gene sequencing to explore the dynamic changes in the fecal bacterial communities and functions in 120 broilers from 4 to 16 weeks of age. We found that the main phyla (Firmicutes, Fusobacteria, Proteobacteria, and Bacteroides) accounted for more than 93.5% of the total bacteria in the feces. The alpha diversity of the fecal microbiota showed a downward trend with time, and the beta diversity showed significant differences at various time points. Then, the study on the differences of microbiota between high-weight (HW) and low-weight (LW) broilers showed that there were differences in the diversity and composition of microbiota between high- and low-weight broilers. Furthermore, we identified 22 genera that may be related to the weight change of broilers. The analysis of flora function reveals their changes in metabolism, genetic information processing, and environmental information processing. Finally, combined with microbial function and cecal transcriptome results, we speculated that microorganisms may affect the immune level and energy metabolism level of broilers through their own carbohydrate metabolism and lipid metabolism and then affect body weight (BW). Our results will help to expand our understanding of intestinal microbiota and provide guidance for the production of high-quality broilers. IMPORTANCE The intestinal microbiota has a certain impact on the performance of broilers. However, the change of intestinal microbiota after 4 weeks of age is not clear, and the mechanism of the effect of microorganisms on the weight change of broilers needs more exploration. After 4 weeks of age, the alpha diversity of microorganisms in broiler feces decreased, and the dominant bacteria were Firmicutes, Fusobacteria, Proteobacteria, and Bacteroides. There were differences in microbiota diversity and composition between high- and low-weight broilers. Intestinal microorganisms may affect the immune level and energy metabolism level of broilers through their own carbohydrate metabolism and lipid metabolism and then affect the body weight. The results are helpful to increase the understanding of intestinal microbiota and provide reference for the production of high-quality broilers.

Microbiome, Transcriptome, and Metabolomic Analyses Revealed the Mechanism of Immune Response to Diarrhea in Rabbits Fed Antibiotic-Free Diets

In this study, diarrhea was induced in rabbits by feeding them antibiotic-free feed. The gut provides important defense against the barriers of the body, of which the duodenum is an important part to help digest food and absorb nutrients. However, the mechanisms underlying the roles of the gut microbiome and fecal metabolome in rabbit diarrhea caused by feeding an antibiotic-free diet have not been characterized. Recently, only a single study has been conducted to further characterize the antibiotic-free feed additives that caused diarrhea in weaned rabbits. The multi-omics techniques, including 16S rRNA sequencing, transcriptome sequencing, and LC-MS analysis, were combined to analyze the gut microbial compositions and functions. They also determined the fecal metabolomic profiles of diarrhea in rabbits caused by feeding antibiotic-free feed. The results showed that the liver, duodenal, and sacculus rotundus tissues of diarrhea rabbits were diseased, the composition of intestinal microbes was significantly changed, the diversity of intestinal microbes was decreased, and the distribution of intestinal microbe groups was changed. Functional analysis based on the cluster of GO and KEGG annotations suggested that two functional GO categories belonged to the metabolism cluster, and five KEGG pathways related to the metabolic pathways were significantly enriched in diarrhea rabbits. Moreover, real-time quantitative PCR (RT-qPCR) was used to verify the significant expression of genes related to diarrhea. Metabolomics profiling identified 432 significantly differently abundant metabolites in diarrhea rabbits, including amino acids and their derivatives. These amino acids were enriched in the tryptophan metabolic pathway. In addition, the functional correlation analysis showed that some altered gut microbiota families, such as Parasutterella, significantly correlated with alterations in fecal metabolites. Collectively, the results suggested that altered gut microbiota was associated with diarrhea caused by antibiotic-free feed additives in weaned rabbit pathogenesis.

Phosphorus Restriction in Brooding Stage Has Continuous Effects on Growth Performance and Early Laying Performance of Layers

Simple Summary

Phosphorus plays a critical role in bone and eggshell formation. Dietary phosphorus oversupply depletes non-renewable natural resources and causes environmental concerns in animal husbandry. This study evaluated the effects of phosphorus restriction in the brooding stage and subsequent recovery on growth performance, tibia development and early laying performance of layers. Phosphorus restriction decreases growth performance and bone characters in the brooding stage, and the adverse effects on body weight and early laying performance do not disappear after phosphorus supplementation. These findings give a foundation and new perspective on low phosphorus feeding strategies in the production of layers.

Abstract

This study evaluated the effects of phosphorus restriction in the brooding stage and subsequent recovery on growth performance, tibia development and early laying performance of layers. 360 one-day-old hens were randomly divided into 4 groups with 6 replicates and 15 chicks per replicate. Chicks were fed diets containing 0.13% (L), 0.29% (M), 0.45% (N), 0.59% (H) non-phytate phosphorus (nPP) from 1 to 8 weeks of age. From 9 to 20 weeks of age, the L and N group were divided into two groups fed normal level phosphorus (n, 0.39% nPP) and high-level phosphorus (h, 0.45% nPP) separately, then all the birds were fed a normal diet (0.39% nPP) from 21 to 26 weeks of age. Four treatments were tested: Ln, Lh, Nn, and Nh. The lower body weight, average daily feed intake, tibia length and daily tibial increment were observed in the L group (p < 0.05) and the ratio of feed to gain was significantly increased in the L group at 8 weeks of age (p < 0.05). In addition, the fresh and degreased tibia weight, bone ash, Ca content in the tibia and P content in the ash and tibia were significantly decreased in the L group at 8 weeks of age (p < 0.05). After compensatory processes, there was no significant difference in tibia characters; however, body weight in the Ln group was significantly lower than in the Nn group (p < 0.05) and was significantly lower in the Lh group than the Nn group (p < 0.01) and Nh group (p < 0.05). In addition, the laying rate and average daily egg mass in the Lh group were lower than Nn and Nh (p < 0.05). In conclusion, severe dietary phosphorus restriction impaired growth performance and bone mineralization in the brooding stage. Subsequent phosphorus supplementation could not alleviate this adverse effect on body weight, which continued to affect egg production. These findings give a foundation and new perspective on a low phosphorus feeding strategy in layer production.