Microbial community and short-chain fatty acid profile in gastrointestinal tract of goose

Prebiotic characteristics of degraded polysaccharides from Acanthopanax senticosus polysaccharide on broilers gut microbiota based on in vitro digestion and fecal fermentation

This study aimed to evaluate the effect of low molecular weight Acanthopanax polysaccharides on simulated digestion, probiotics, and intestinal flora of broilers in vitro. The experiments were carried out by H2O2-Vc degradation of Acanthopanax polysaccharides, in vitro simulated digestion to evaluate the digestive performance of polysaccharides with different molecular weights, in vitro probiotic evaluation of the probiotic effect of polysaccharides on lactobacilli and bifidobacteria, in vitro anaerobic fermentation and high-throughput sequencing of 16S rRNA genes to study the impact of Acanthopanax polysaccharides on the intestinal flora of broilers, and the effect of Acanthopanax polysaccharides on the short-chain fatty acids of intestines were determined by GC-MS method. The results showed that the molecular weight of Acanthopanax polysaccharide (ASPS) was 9,543 Da, and the molecular weights of polysaccharides ASPS-1 and ASPS-2 were reduced to 4,288 Da and 3,822 Da after degradation, and the particle sizes, PDIs, and viscosities were also significantly decreased. ASPS-1 has anti-digestive properties and better in vitro probiotic properties. The addition of ASPS-1 regulates the structure of intestinal microorganisms by regulating fecalibacterium to produce short-chain fatty acids, promoting the colonization of beneficial bacteria such as fecalibacterium, paraprevotella and diminishing the prevalence of detrimental bacteria such as Fusobacteria. Interestingly the ASPS-1 group found higher levels of Paraprevotella, which degraded trypsin in the gut, reducing inflammation, acted as a gut protector, and was influential in increasing the levels of acetic acid, propionic acid, butyric acid, isobutyric acid, valeric acid, and total SCFAs in the fermented feces. Therefore, the degraded ASPS-1 can better regulate the structure of intestinal flora and promote the production of SCFAs, creating possibilities for its use as a potential prebiotic, which is conducive to the intestinal health of poultry.

Yaks Are Dependent on Gut Microbiota for Survival in the Environment of the Qinghai Tibet Plateau

The yak (Poephagus grunniens) has evolved unique adaptations to survive the harsh environment of the Qinghai-Tibetan Plateau, while their gut microorganisms play a crucial role in maintaining the health of the animal. Gut microbes spread through the animal population not only by horizontal transmission but also vertically, which enhances microbial stability and inheritance between generations of the population. Homogenization of gut microbes in different animal species occurs in the same habitat, promoting interspecies coexistence. Using the yak as a model animal, this paper discusses the adaptive strategies under extreme environments, and how the gut microbes of the yak circulate throughout the Tibetan Plateau system, which not only affects other plateau animals such as plateau pikas, but can also have a profound impact on the health of people. By examining the relationships between yaks and their gut microbiota, this review offers new insights into the adaptation of yaks and their ecological niche on the Qinghai-Tibetan plateau.

Effects of rearing systems (cage versus floor) on the microbial composition and transcriptome of goose ileum

There is a gradual transition from water to dryland rearing of geese. In this study, we performed 16S rRNA sequencing (16S rRNA-seq) and transcriptome sequencing (RNA-seq) to reveal the effects of cage rearing (CR) and floor rearing (FR) systems on the microbial composition and transcriptome of the goose ileum. Through 16S rRNA-seq, Linear Discriminant Analysis Effect Size (LEfSe) analysis identified 2 (hgcI_clade and Faecalibacterium) and 14 (Bacteroides, Proteiniphilum, Proteiniclasticum, etc.) differential microbiota in CR and FR, respectively. The rearing system influenced 4 pathways including biosynthesis of amino acids in ileal microbiota. Moreover, we identified 1,198 differentially expressed genes (DEGs) in the ileum mucosa, with 957 genes up-regulated in CR and 241 genes up-regulated in FR. In CR, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the significant enrichment (p < 0.05) of 28 KEGG pathways, most of which were associated with amino acid metabolism. In FR, up-regulated DEGs were mainly enriched in KEGG pathways associated with cellular processes, including apoptosis, necroptosis, and cellular senescence. Spearman correlation analysis of differential microbiota and amino acid metabolism-related DEGs in CR showed a significant positive correlation. Additionally, differential microbiota of FR, Phascolarctobacterium and Sutterella, were positively correlated with FGF10 (p < 0.05) and PIK3R1 (p < 0.01), respectively. In conclusion, there might be differences in ileal amino acid metabolism levels between CR and FR geese, and the observed increase in harmful bacterial species in FR might impact the activity of ileal cells.

In-depth investigation of the therapeutic effect of Tribulus terrestris L. on type 2 diabetes based on intestinal microbiota and feces metabolomics

ETHNOPHARMACOLOGICAL RELEVANCE

The fruit of Tribulus terrestris L. (TT) is extensively documented in the Tibetan medical literature 'Si Bu Yi Dian', has been used to treat diabetes mellitus for more than a thousand years. However, the underlying mechanisms and comprehensive effects of TT on diabetes have yet to be investigated.

AIM OF THE STUDY

The aim of the study was to systemically elucidate the potential mechanisms of TT in treating diabetes mellitus, and further investigate the therapeutic effects of the water extract, small molecular components and saccharides from TT.

MATERIALS AND METHODS

Fecal metabolomics was employed to draw the metabolic profile based on UHPLC-Q-TOF-MS/MS. The V3-V4 hypervariable regions of the bacteria 16S rRNA gene were amplified to explore the structural changes of the intestinal microbiome after TT intervention and to analyze the differential microbiota. The microbial metabolites SCFAs were determined by GC-MS, and the BAs and tryptophan metabolites were quantified by UPLC-TQ-MS. Spearman correlation analysis was carried out to comprehensively investigate the relationship among the endogenous metabolites profile, intestinal microbiota and their metabolites.

RESULTS

TT exhibited remarkably therapeutic effect on T2DM rats, as evidenced by improved glucolipid metabolism and intestinal barrier integrity, ameliorated inflammation and remission in insulin resistance. A total of 24 endogenous biomarkers were screened through fecal metabolomics studies, which were mainly related to tryptophan metabolism, fatty acid metabolism, bile acid metabolism, steroid hormone biosynthesis and arachidonic acid metabolism. Investigations on microbiomics revealed that TT significantly modulated 18 differential bacterial genera and reversed the disordered gut microbial in diabetes rats. Moreover, TT notably altered the content of gut microbiota metabolites, both in serum and fecal samples. Significant correlation among microbial community, metabolites and T2DM-related indicators was revealed.

CONCLUSIONS

The multiple components of TT regulate the metabolic homeostasis of the organism and the balance of intestinal microbiota and its metabolites, which might mediate the anti-diabetic capacity of TT.

Avian influenza and gut microbiome in poultry and humans: A "One Health" perspective

A gradual increase in avian influenza outbreaks has been found in recent years. It is highly possible to trigger the next human pandemic due to the characteristics of antigenic drift and antigenic shift in avian influenza virus (AIV). Although great improvements in understanding influenza viruses and the associated diseases have been unraveled, our knowledge of how these viruses impact the gut microbiome of both poultry and humans, as well as the underlying mechanisms, is still improving. The "One Health" approach shows better vitality in monitoring and mitigating the risk of avian influenza, which requires a multi-sectoral effort and highlights the interconnection of human health with environmental sustainability and animal health. Therefore, monitoring the gut microbiome may serve as a sentinel for protecting the common health of the environment, animals, and humans. This review summarizes the interactions between AIV infection and the gut microbiome of poultry and humans and their potential mechanisms. With the presented suggestions, we hope to address the current major challenges in the surveillance and prevention of microbiome-related avian influenza with the "One Health" approach.

Metagenomic Analysis Reveals A Gut Microbiota Structure and Function Alteration between Healthy and Diarrheic Juvenile Yaks

Diarrhea-induced mortality among juvenile yaks is highly prevalent in the pastoral areas of the Qinghai-Tibet plateau. Although numerous diseases have been linked to the gut microbial community, little is known about how diarrhea affects the gut microbiota in yaks. In this work, we investigated and compared changes in the gut microbiota of juvenile yaks with diarrhea. The results demonstrated a considerable drop in the alpha diversity of the gut microbiota in diarrheic yaks, accompanied by Eysipelatoclostridium, Parabacteroides, and Escherichia-Shigella, which significantly increased during diarrhea. Furthermore, a PICRust analysis verified the elevation of the gut-microbial metabolic pathways in diarrhea groups, including glycine, serine, and threonine metabolism, alanine, aspartate, oxidative phosphorylation, glutamate metabolism, antibiotic biosynthesis, and secondary metabolite biosynthesis. Taken together, our study showed that the harmful bacteria increased, and beneficial bacteria decreased significantly in the gut microbiota of yaks with diarrhea. Moreover, these results also indicated that the dysbiosis of the gut microbiota may be a significant driving factor of diarrhea in yaks.

Dietary Paper Mulberry Silage Supplementation Improves the Growth Performance, Carcass Characteristics, and Meat Quality of Yangzhou Goose

There have been few investigations into the health benefits and meat quality of supplementing Yangzhou geese with paper mulberry silage. One hundred and twenty 28-day-old Yangzhou geese were selected for the experiment and randomly divided into two groups: a control group (CON) and a paper mulberry silage group (PM), with six replicates in each group. The experiment lasted for a total of 6 weeks. The experiment found that compared with CON, PM had a promoting effect on the average daily weight gain of Yangzhou geese (p = 0.056). Sensory and nutritional analysis of breast muscles revealed a decrease in a* value (p < 0.05) and an increase in protein content (p < 0.05) following PM treatment. Through untargeted metabolomics analysis of breast muscle samples, it was found that 11 different metabolites, including guanidinoacetic acid and other substances, had a positive effect on amino acid metabolism and lipid antioxidant pathways of PM treatment. Overall, the strategy of feeding Yangzhou geese with paper mulberry silage is feasible, which can improve the sensory quality and nutritional value of goose meat. The experiment provides basic data for the application form of goose breeding, so exploring the impact of substances within paper mulberry on goose meat should be focused on in the future.

Differences in the microbiome of the small intestine of Leghorn lines divergently selected for antibody titer to sheep erythrocytes suggest roles for commensals in host humoral response

For forty generations, two lines of White Leghorn chickens have been selected for high (HAS) or low (LAS) antibody response to a low dose injection of sheep red blood cells (SRBCs). Their gut is home to billons of microorganisms and the largest number of immune cells in the body; therefore, the objective of this experiment was to gain understanding of the ways the microbiome may influence the differential antibody response observed in these lines. We achieved this by characterizing the small intestinal microbiome of HAS and LAS chickens, determining their functional microbiome profiles, and by using machine learning to identify microbes which best differentiate HAS from LAS and associating the abundance of those microbes with host gene expression. Microbiome sequencing revealed greater diversity in LAS but statistically higher abundance of several strains, particularly those of Lactobacillus, in HAS. Enrichment of microbial metabolites implicated in immune response such as lactic acid, short chain fatty acids, amino acids, and vitamins were different between HAS and LAS. The abundance of several microbial strains corresponds to enriched host gene expression pathways related to immune response. These data provide a compelling argument that the microbiome is both likely affected by host divergent genetic selection and that it exerts influence on host antibody response by various mechanisms.

Metagenomic reconstructions of caecal microbiome in Landes, Roman and Zhedong White geese

1. The caecal microbiota in geese play a crucial role in determining the host's health, disease status and behaviour, as evidenced by extensive epidemiological data. The present investigation conducted 10× metagenomic sequencing of caecal content samples obtained from three distinct goose species, namely Landes geese, Roman geese and Zhedong White geese (n = 5), to explore the contribution of the gut microbiome to carbohydrate metabolism.2. In total, 337GB of Illumina data were generated, which identified 1,048,575 complete genes and construction of 331 metagenomic bins, encompassing 78 species from nine phyla. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Bacteria were identified as the dominant phyla while Prevotella, Bacteroides, Streptococcus, and Subdoligranulum were the most abundant genera in the caecum of geese.3. The genes were allocated to 375 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) analysis. The most abundant classes in the caecum of geese were confirmed to be glycoside hydrolases (GHs), glycosyl transferases (GTs), as identified through the carbohydrate-active enzyme (CAZyme) database mapping. Subdoligranulum variabile and Mediterraneibacter glycyrrhizinilyticus were discovered to potentially facilitate carbohydrate digestion in geese.4. Notwithstanding, further investigation and validation are required to establish a connection between these species and CAZymes. Based on binning analysis, Mediterraneibacter glycyrrhizinilyticus and Ruminococcus sp. CAG:177 are potential species in LD geese that contribute to the production of fatty liver.

Slaughter performance of the main goose breeds raised commercially in China and nutritional value of the meats of the goose breeds: a systematic review

A number of goose breeds are raised commercially in China. However, the data on the slaughter performance of the goose breeds and the nutritional value of their meats lack a thorough comparative analysis. In this systematic review, the slaughter performance of the goose breeds and nutritional value of their meats were comparatively analyzed to provide an overview of the characteristics of the goose breeds raised commercially in China. Fifteen goose breeds were selected from 27 research articles published up to January 2022 on the slaughter performance of the goose breeds raised commercially in China and their nutrient composition after literature searching, literature screening, variety selection, and data collation. The slaughter indexes of the goose breeds and the basic nutrient composition, amino acid composition, and fatty acid composition of the meats of the goose breeds were standardized using min-max normalization and compared. The results suggest that the slaughter indexes and nutritional indicators of the meats of Yangzhou white goose, Xupu goose, Landaise geese, and Sichuan white goose are more balanced than those of the meats of the other goose breeds. The results of this review can lay the foundation for optimizing the breeding methods of the commercially raised goose breeds and processing methods of the meats of the geese. © 2022 Society of Chemical Industry.

Effects of indoor and outdoor rearing system on geese biochemical parameters and cecal microbial composition

The present study aimed to investigate the impact of indoor and outdoor rearing systems on the biochemistry and microbial composition of White Roman geese, with a particular focus on the gut microbiome. Our results showed that geese reared in an outdoor system had significantly lower serum aspartate aminotransferase (AST) compared to those reared indoors, but lower levels of high-density lipoprotein (HDL) and higher levels of low-density lipoprotein (LDL). Moreover, the cecal microbiota of geese reared outdoors exhibited higher species evenness and increased alpha diversity, with a significant alteration in the F/B ratios. The bacterial taxonomy composition also differed between the 2 rearing systems, with higher relative abundances of the Firmicutes and Actinobacteria and lower relative abundances of the Bacteroidetes and Proteobacteria in the outdoor system. These findings suggest that rearing systems may play a critical role in shaping the gut microbiome and overall health of geese. Notably, our data demonstrated that indoor rearing was associated with a higher abundance of pathogenic genera and a lower abundance of commensal genera compared to outdoor rearing. Our study supports the hypothesis that rearing systems may alter the physiological functions and microbial composition of geese, and highlights the need for further research to confirm and expand upon these findings. In summary, our study underscores the importance of considering the impact of rearing systems on the gut microbiome and health of geese.

Abrupt Dietary Change and Gradual Dietary Transition Impact Diarrheal Symptoms, Fecal Fermentation Characteristics, Microbiota, and Metabolic Profile in Healthy Puppies

Dietary changes are inevitable for pets, yet little is known about the impact of different dietary change methods on the gastrointestinal response. The current comparative study evaluated the effects of different dietary changes on the diarrheal symptoms, fecal fermentation characteristics, microbiota, and metabolic profile of healthy puppies. A total of 13 beagle puppies were randomly divided into two groups; puppies in the abrupt change (AC) group were given 260 g of a chicken- and duck-based extruded diet (CD)daily for the one-week transition period, whereas puppies in the gradual transition (GT) group were fed according to a gradual transition ratio of a salmon-based extruded diet (SA) and a CD diets with a difference of 40 g per day for seven consecutive days. Serum samples were collected on D7, and fecal samples were collected on D0 and D7. The results indicated that GT reduced the incidence of diarrhea in puppies throughout the trial period. Dietary change methods had no influence on serum inflammatory factors or fecal SCFAs, but isovaleric acid was significantly reduced after GT. Meanwhile, 16S rRNA sequencing showed that the fecal microbiota was changed after different dietary changes. Compared with the bacterial changes after AC, the relative abundances of beneficial bacteria (i.e., Turicibacter and Faecalibacterium) in feces were increased after GT in puppies. Additionally, both GT and AC caused changes in amino acid metabolism, while AC also altered lipid metabolism. AC increased fecal histamine and spermine concentrations, but decreased concentrations of metabolites such as 5-hydroxyindoleacetic acid and serotonin. Our findings indicated that GT most likely reduced the diarrhea rate in puppies by modulating the composition and metabolism of the gut microbiota.

The integrated analysis of digestive physiology and gastrointestinal microbiota structure in Changle goose

Changle goose in Fujian, China is a rare genetic resource and in urgent need to be protected. Understanding the characteristics of digestive physiology and spatial variation of gastrointestinal microbiota is crucial for developing nutritional intervention strategies to improve intestinal health and production performance of goose. Hence, histomorphological assay was used for observing development status of proventriculus, jejunum, and cecum in 70-day-old Changle geese, whereas digesta from 6 alimentary canal locations (crop, proventriculus, gizzard, jejunum, cecum, and rectum) were collected for 16S rRNA gene sequencing and short chain fatty acids (SCFAs) quantitative analysis. The histomorphological observation indicated that the jejunum and cecum of Changle goose were well developed. The alpha diversity analysis revealed that, except rectum, microbiota in other noncecum sections were in high diversity as cecum. The Nonmetric MultiDimensional Scaling (NMDS) analysis showed that microbial community of proventriculus, gizzard, and jejunum formed a cluster, which distinctly discrete with the microbiota of the other gastrointestinal locations. Additionally, the proportions of Proteobacteria, Bacteroidota, and Campilobacterota at the phylum level and Lactobacillus, Streptococcus, Helicobacter, and Subdoligranulum at the genus level exhibited tremendous alternations among different gastrointestinal locations. The characteristic bacterial composition in each section was further disclosed by analyzing the core and feature Amplicon Sequence Variants (ASVs) and SCFAs pattern. Importantly, 7 body-weight-associated ASVs and 2 cecum-development-related ASVs were identified via correlation analysis. In a whole, our findings provided the first insights into the specialized digestive physiology of Changle geese and distinctive regional distribution of gastrointestinal microbiota, which laid the important foundation for improving growth performance through microbiota manipulation in geese.

Comparison of the caecal microbial community structure and physiological indicators of healthy and infection Eimeria tenella chickens during peak of oocyst shedding

Eimeria tenella (E. tenella), an important intestinal parasite of chicken caeca, causes coccidiosis and brings large economic losses to the poultry industry annually. Gut microorganismal alterations directly affect the health of the body. To understand how E. tenella affects its host, we analysed the changes in caecal microbial diversity and the physiological and morphological changes during the peak of oocyst shedding. Infected and healthy chickens differed significantly in caecal pathology and blood indicators. At the genus level, the abundances of Faecalibacterium, Clostridium, Lachnoclostridium, Gemmiger, Flavonifractor, Pseudoflavonifractor and Oscillibacter were significantly decreased in the infected samples, whereas Escherichia, Nocardia and Chlamydia were significantly increased. Functional gene pathways related to replication, recombination and repair, and transcription were significantly decreased, and functional genes related to metabolism were highly significantly reduced in the infected samples. Furthermore, in the infected samples, E. tenella reduced the haemoglobin levels and red blood cell counts, greatly reduced the beneficial bacteria and increased the potentially pathogenic bacteria. This study provides a research basis for further understanding the pathogenic mechanisms of E. tenella and provides insight for potential new drug development.RESEARCH HIGHLIGHTS First simultaneous description of caecal microbiota and physiological indicators during E. tenella infection.Metagenomics used to explore functional properties of chicken caecal microbiota during E. tenella infection.Caecal microbial compositions and functional genes altered significantly after infection.Blood indicators and caecal morphology were significantly altered in the infected group.

Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes

16S rRNA amplicon sequences are predominantly used to identify the taxonomic composition of a microbiome, but they can also be used to generate simulated metagenomes to circumvent costly empirical shotgun sequencing. The effectiveness of using "simulated metagenomes" (shotgun metagenomes simulated from 16S rRNA amplicons using a database of full genomes closely related to the amplicons) in nonmodel systems is poorly known. We sought to determine the accuracy of simulated metagenomes in a nonmodel organism, the Canada goose (Branta canadensis), by comparing metagenomes and metatranscriptomes to simulated metagenomes derived from 16S amplicon sequencing. We found significant differences between the metagenomes, metatranscriptomes, and simulated metagenomes when comparing enzymes, KEGG orthologies (KO), and metabolic pathways. The simulated metagenomes accurately identified the majority (>70%) of the total enzymes, KOs, and pathways. The simulated metagenomes accurately identified the majority of the short-chain fatty acid metabolic pathways crucial to folivores. When narrowed in scope to specific genes of interest, the simulated metagenomes overestimated the number of antimicrobial resistance genes and underestimated the number of genes related to the breakdown of plant matter. Our results suggest that simulated metagenomes should not be used in lieu of empirical sequencing when studying the functional potential of a nonmodel organism's microbiome. Regarding the function of the Canada goose microbiome, we found unexpected amounts of fermentation pathways, and we found that a few taxa are responsible for large portions of the functional potential of the microbiome. IMPORTANCE The taxonomic composition of a microbiome is predominately identified using amplicon sequencing of 16S rRNA genes, but as a single marker, it cannot identify functions (genes). Metagenome and metatranscriptome sequencing can determine microbiome function but can be cost prohibitive. Therefore, computational methods have been developed to generate simulated metagenomes derived from 16S rRNA sequences and databases of full-length genomes. Simulated metagenomes can be an effective alternative to empirical sequencing, but accuracy depends on the genomic database used and whether the database contains organisms closely related to the 16S sequences. These tools are effective in well-studied systems, but the accuracy of these predictions in a nonmodel system is less known. Using a nonmodel bird species, we characterized the function of the microbiome and compared the accuracy of 16S-derived simulated metagenomes to sequenced metagenomes. We found that the simulated metagenomes reflect most but not all functions of empirical metagenome sequencing.

The Effects of Dietary Bacillus amyloliquefaciens TL106 Supplementation, as an Alternative to Antibiotics, on Growth Performance, Intestinal Immunity, Epithelial Barrier Integrity, and Intestinal Microbiota in Broilers

A total of 240 1-day-old Arbor Acres male broilers were randomly divided into five dietary treatments (control feed (CON), supplemented with 75 mg/kg aureomycin (ANT), supplemented with 7.5 × 108 CFU/kg (Ba1) and 2.5 × 109 CFU/kg (Ba1), and 7.5 × 109 CFU/kg (Ba3) Bacillus amyloliquefaciens TL106, respectively) to investigate the probiotic effect of TL106 instead of antibiotics in broilers. On days 1−21, the average daily gain of broilers in the Ba groups was increased compared with the CON group (p < 0.05). In addition, the feed/gain ratio of broilers in the Ba groups was lower than that of broilers in the CON and ANT groups on days 22−42 and days 1−42 (p < 0.05). Compared with the CON group, dietary TL106 increased the digestibility of crude fiber and crude protein (p < 0.05), and the effect was similar to that of the ANT group. The levels of IL-1β, IFN-γ, and IL-6 in serum, jejunum, and ileum of broilers fed TL106 were decreased compared with the control group (p < 0.05). The mRNA expression of tight junction proteins in broilers of ANT and Ba groups was higher than the control group (p < 0.05). After 21 days, villus height and the ratio of villus height to crypt depth of duodenum and jejunum of broilers fed TL106 were higher than the control group (p < 0.05). The concentrations of short-chain fatty acids such as lactate, acetate, propionate, and butyrate in cecal digesta of broilers dietary TL106 were higher than the control group (p < 0.05). The supplementation with TL106 altered the compositions and diversity of the cecal microbiota of broilers. Moreover, supplementation with TL106 improved the ratio of Firmicutes to Bacteroidetes and decreased the relative abundance of Proteobacteria on days 21 and 28, while the abundance of Peptostreptococcaceae, Ruminococcaceae and Lactobacillaceae was increased. On days 35 and 42, broilers fed TL106 had an increased total abundance of Firmicutes and Bacteroidetes and decreased abundances of Lactobacillaceae, while the abundance of Barnesiellaceae was increased. In conclusion, dietary supplementation with TL106 improved the broiler’s growth performance, immune response capacity, gut health, modulated development, and composition of the gut microbiota in broilers. It is suggested that Bacillus amyloliquefaciens TL106 may be a suitable alternative to in-feed antibiotics to improve broiler health and performance.

Environmental exposure to swine farms reshapes human gut microbiota

The gut microbiota can change to varying degrees because of changes in the environment. In the present study, we performed microbial amplicon sequencing on the feces of people who had long-term exposure to swine farms (F) and that of people living in normal environments (S) to investigate the impact of the environment on the human gut microbiota. A total of 1,283,503 high-quality ordered sequences were obtained, which provided different levels of microbial classification and statistics. We found that different environments did not alter the richness and diversity of the microbial communities in participants, but caused significant changes in the proportion of some bacteria. The main bacterial phyla found in group F participants were Firmicutes (69.44-89.03%), Actinobacteria (1.7-18.95%), and Bacteroidetes (1.17-22.35%); those found in group S participants were Firmicutes (49.93-95.04%), Bacteroidetes (0.62-39.59%), and Proteobacteria (0.98-11.95%). Additionally, because of changes in phylum proportions, the Bugbase phenotypic classification predicted an increase in the proportion of Gram-positive bacteria in group F and an increase in the proportion of Gram-negative bacteria in group S. In conclusion, our findings suggest that human exposure to swine farms can reshape the gut microbiota, resulting in changes in the microbial abundances. This change can potentially reduce the odds of developing bowel disease and contribute to the prevention of intestinal diseases, providing a theoretical basis for improving human health.

Effects of Dietary Essential Oils Supplementation on Egg Quality, Biochemical Parameters, and Gut Microbiota of Late-Laying Hens

The objective of this study was to explore the effects of adding essential oils (EO) to diets on egg quality, biochemical parameters and intestinal flora of late laying hens. The number of 252 Dawu Golden Phoenix laying hens (55 weeks old) were randomly sorted into two groups: the control group (CG) fed a basal diet and the EO group fed a basal diet with 300 mg/kg of essential oils. The average egg weight, feed-to-egg ratio, and egg production rate were determined every week. The trial started at week 55 and lasted for 8 weeks. During the experiment’s last week, 36 eggs out of each group were chosen at random to test. In our study, dietary supplementation with EO considerably decreased the egg breaking rate (p = 0.01) and increased the shell-breaking strength (p = 0.04). The treatment group’s alanine aminotransferase (ALT) levels were considerably lower than those of the control group (p = 0.03). The EO group had substantially higher total antioxidant capacity (T-AOC) and total superoxide dismutase (T-SOD) (p = 0.04 and p =0.03, respectively). However, there were no differences in alpha diversity indicators between the two groups. It is worth noting that Firmicutes were increased considerably (p < 0.05), while Spirochaetota and Proteobacteria were significantly reduced in the EO group. At genus levels, the EO supplementation increased the relative abundance of Intestinimonas (p < 0.05) and Megamonas (p < 0.01). In conclusion, a dietary supplementation of 300 mg/kg EO can improve the production performance of laying hens and the egg quality. It can also regulate the abundance of cecal flora and serum biochemical indicators.

Pesticide thiram exposure alters the gut microbial diversity of chickens

Thiram is a major dithiocarbamate pesticide commonly found in polluted field crops, feed, and rivers. Environmental thiram exposure has been demonstrated to cause angiogenesis and osteogenesis disorders in chickens, but information regarding thiram influences on gut microbiota, apoptosis, and autophagy in chickens has been insufficient. Here, we explored the effect of thiram exposure on gut microbiota, apoptosis, and autophagy of chickens. Results demonstrated that thiram exposure impaired the morphology and structure of intestinal and liver tissues. Moreover, thiram exposure also triggered liver apoptosis and autophagy. The gut microbiota in chickens exposed to thiram exhibited a significant decline in alpha diversity, accompanied by significant shifts in taxonomic compositions. Bacterial taxonomic analysis indicated that thiram exposure causes a significant reduction in the levels of eight genera, as well as a significant increase in the levels of two phyla and 10 genera. Among decreased bacterial genera, seven genera even cannot be observed in the thiram-induced chickens. In summary, this study demonstrated that thiram exposure not only dramatically altered the gut microbial diversity and composition but also induced liver apoptosis and autophagy in chickens. Importantly, this study also conveyed a key message that the dysbiosis of gut microbiota may be one of the major pathways for thiram to exert its toxic effects.

Effects of fulvic acid addition on laying performance, biochemical indices, and gut microbiota of aged hens

The purpose of this study was to appraise the effect of fulvic acid on production, biochemical indices, and gut microbiota of laying hens. A total of 252 Dawu Golden Phoenix laying hens (55-week-old) were allotted to two treatments randomly, each with six replicates and 21 hens per replicate, including the control group (CG) and fulvic acid (500 mg/kg) group (FA). The trial period was 8 weeks. Adding FA raised egg weight (P = 0.03), shell-breaking strength (P = 0.03), and reduced egg breaking rate (P < 0.01), compared with CG. There was no difference in eggshell thickness and egg shape index between the two treatments; however, the FA group increased egg production by 1.45% and reduced the feed-to-egg ratio by 0.09. Moreover, dietary FA decreased the aspartate aminotransferase levels in serum (P = 0.04), and glutathione peroxidase and total antioxidant capacity were increased (P = 0.02 and 0.04, respectively). Despite this, the two groups had no differences in the alpha diversity indices (PD_whole trees, Shannon, Ace, Simpson, Chao1, and goods_coverage). Obviously, at the phylum level, the abundances of Firmicutes were improved (P < 0.01), Actinobacteriota (P < 0.01), and Proteobacteria (P < 0.01) were reduced by dietary FA. Supplementation with FA could improve the abundances of Megamonas (P < 0.01) and reduce Enterobacter (P < 0.01) at the genus level. To sum up, this study showed the addition of 500 mg/kg FA may boost production and egg quality and modulate the cecal microflora abundance and serum biochemical indices of laying hens.

The avian gut microbiota: Diversity, influencing factors, and future directions

The gut microbiota is viewed as the “second genome” of animals, sharing intricate relationships with their respective hosts. Because the gut microbial community and its diversity are affected by many intrinsic and extrinsic factors, studying intestinal microbes has become an important research topic. However, publications are dominated by studies on domestic or captive birds, while research on the composition and response mechanism of environmental changes in the gut microbiota of wild birds remains scarce. Therefore, it is important to understand the co-evolution of host and intestinal bacteria under natural conditions to elucidate the diversity, maintenance mechanisms, and functions of gut microbes in wild birds. Here, the existing knowledge of gut microbiota in captive and wild birds is summarized, along with previous studies on the composition and function, research methods employed, and factors influencing the avian gut microbial communities. Furthermore, research hotspots and directions were also discussed to identify the dynamics of the avian gut microbiota, aiming to contribute to studies of avian microbiology in the future.

Chicken Gut Microbiota Responses to Dietary Bacillus subtilis Probiotic in the Presence and Absence of Eimeria Infection

Coccidiosis is a well-known poultry disease that causes the severe destruction of the intestinal tract, resulting in reduced growth performance and immunity, disrupted gut homeostasis and perturbed gut microbiota. Supplementation of probiotics were explored to play a key role in improving growth performance, enhancing innate and adaptive immunity, maintaining gut homeostasis and modulating gut microbiota during enteric infection. This study was therefore designed to investigate the chicken gut whole microbiota responses to Bacillus subtilis (B. subtilis) probiotic feeding in the presence as well as absence of Eimeria infection. For that purpose, 84 newly hatched chicks were assigned into four groups, including (1) non-treated non-challenged control group (CG − ET), (2) non-treated challenged control group (CG + ET), (3) B. subtilis-fed non-challenged group (BS − ET) and (4) B. subtilis-fed challenged group (BS + ET). CG + ET and BS + ET groups were challenged with Eimeria tenella (E. tenella) on 21 day of housing. Our results for Alpha diversity revealed that chickens in both infected groups (CG + ET and BS + ET) had lowest indexes of Ace, Chao 1 and Shannon, while highest indexes of Simpson were found in comparison to non-challenged groups (CG − ET and BS − ET). Firmicutes was the most affected phylum in all experimental groups following Proteobacteria and Bacteroidota, which showed increased abundance in both non-challenged groups, whereas Proteobacteria and Bacteroidota affected both challenged groups. The linear discriminant analysis effect size method (lEfSe) analysis revealed that compared to the CG + ET group, supplementation of probiotic in the presence of Eimeria infection increased the abundance of some commensal genera, included Clostridium sensu stricto 1, Corynebacterium, Enterococcus, Romboutsia, Subdoligranulum, Bacillus, Turicibacter and Weissella, with roles in butyrate production, anti-inflammation, metabolic reactions and the modulation of protective pathways against pathogens. Collectively, these findings evidenced that supplementation of B. subtilis probiotic was positively influenced with commensal genera, thereby alleviating the Eimeria-induced intestinal disruption.

Effects of Yeast Culture Supplementation on Growth Performance, Nutrient Digestibility, Blood Metabolites, and Immune Response in Geese

The present study was conducted to investigate the effects of dietary yeast culture (YC) supplementation on growth performance, nutrient digestibility, blood metabolites, and immune functions in geese. One-day-old Sichuan white geese (n = 300) were randomly divided into five groups containing 0 (control), 0.5%, 1.0%, 2.0%, and 4.0% of YC in the diet for 70 days. In general, the dietary supplementation of YC significantly increased the average daily gain and feed conversion ratio (p < 0.05) in which the 1.0% or 2.0% levels were better and significantly reduced the average daily feed intake at the 2.0% level (p < 0.05). YC supplementation increased digestibility of P (quadratic, p = 0.01) and gross energy (quadratic, p = 0.04) from days 23 to 27 and crude protein from days 23 to 27 and days 64 to 68 (quadratic, p ≤ 0.05), with the 2.0% level being the most effective. Serum metabolites were significantly affected by dietary YC (p < 0.05). Supplemental YC increased IL-2 on day 28 (linear, p = 0.01; quadratic, p = 0.04) and lysozyme on day 70 (quadratic, p = 0.04) and decreased complement C4 on day 70 (linear, p = 0.05). Interferon-γ, interleukin-2, and tumor necrosis factor-α genes were mostly up-regulated after YC supplementation, and interferon-γ and interleukin-2 gene expression levels were significantly increased at the 2.0% level (p < 0.05). Taken together, dietary YC supplementation improved growth performance and affected nutrient digestibility, serum metabolites, and immune function in geese, which was optimized at the 2% YC level in the present study.

Alterations in the Gut Microbial Composition and Diversity of Tibetan Sheep Infected With Echinococcus granulosus

Hydatidosis/cystic echinococcosis (CE) caused by Echinococcus granulosus is a parasitic zoonotic disease worldwide, threatening animal health and production and public health safety. However, it is still unclear that whether E. granulosus infection can result in the alteration of gut microbiota in Tibetan sheep. Therefore, a study was designed to investigate the influences of E. granulosus infection on gut microbiota of Tibetan sheep. A total of 10 ovine small intestinal contents (five from healthy and five from infected) were obtained and subjected to high-throughput sequencing by MiSeq platform. A total of 2,395,641 sequences and 585 operational taxonomic units (OTUs) were identified. Firmicutes and Proteobacteria were the most dominant phyla in all samples. Moreover, the proportions of Armatimonadetes and Firmicutes in the infected Tibetan sheep were significantly decreased, whereas Actinobacteria, Chloroflexi, and Acidobacteria had significantly increased. At the genus level, the Christensenellaceae_R-7_group and Ruminococcaceae_NK4A214_group were the predominant bacterial genera in all the samples. Furthermore, the healthy Tibetan sheep exhibited higher abundances of Intestinimonas, Butyrivibrio, Pseudobutyrivibrio, Ruminococcaceae, Eubacterium_coprostanoligenes_group, Oxobacter, Prevotella_1, Ruminiclostridium_6, Coprococcus_1, Ruminococcus, Lachnospiraceae_UCG-002, Olsenella, and Acetitomaculum, whereas Kocuria, Clostridium_sensu_stricto_1, Slackia, Achromobacter, and Stenotrophomonas levels were lower. In conclusion, our results conveyed an information that E. granulosus infection may cause an increase in pathogenic bacteria and a decrease in beneficial bacteria. Additionally, a significant dynamical change in gut microbiota could be associated with E. granulosus infection.

Microbiome analysis reveals the significant changes in gut microbiota of diarrheic Baer's Pochards (Aythya baeri)

Gut microbiota has been demonstrated to play multiple crucial roles in immunity, physiology, metabolism, and health maintenance. Diarrhea was closely related to the gut microbiota, but information regarding the alterations in gut microbial composition and structure in Baer's Pochard (Aythya baeri) with diarrhea remains scarce. Here, 16S rDNA amplicon sequencing was performed to investigate the gut microbial variability between diarrheic and healthy Baer's Pochard. Results indicated that the gut bacterial community of diarrheic Baer's Pochard showed a distinct decrease in alpha diversity, accompanied by evident changes in taxonomic compositions. Microbial taxonomic analysis revealed that Firmicutes, Proteobacteria and Bacteroidetes were the most dominant phyla in all the fecal samples regardless of health status. At the genus level, the differences in gut bacterial abundance between healthy and diarrheic populations were gradually observed. Specifically, the proportion of Elusimicrobia in the diarrheic Baer's Pochard was increased in comparison with healthy populations, while Acidobacteria, Rokubacteria, Cyanobacteria and Patescibacteria were dramatically decreased. Additionally, the relative proportion of 23 bacterial genera significantly decreased in diarrheic Baer's Pochard, whereas the relative percentage of 4 bacterial genera (Alkanindiges, Elusimicrobium, Spirosoma and Exiguobacterium) observably increased as compared to healthy populations. Taken together, the present study revealed that there were distinct differences in the gut microbial composition and diversity between the healthy and diarrheic Baer's Pochard. Remarkably, this is the first report on the differences in the gut microbiota of Baer's Pochard under different health states and may contribute to provide better insight into gut microbial composition and diversity of Baer's Pochard.

Covariation of the Fecal Microbiome with Diet in Nonpasserine Birds

Opportunistic feeding and multiple other environment factors can modulate the gut microbiome, and bias conclusions, when wild animals are used for studying the influence of phylogeny and diet on their gut microbiomes. Here, we controlled for these other confounding factors in our investigation of the magnitude of the effect of diet on the gut microbiome assemblies of nonpasserine birds. We collected fecal samples, at one point in time, from 35 species of birds in a single zoo as well as 6 species of domestic poultry from farms in Guangzhou city to minimize the influences from interfering factors. Specifically, we describe 16S rRNA amplicon data from 129 fecal samples obtained from 41 species of birds, with additional shotgun metagenomic sequencing data generated from 16 of these individuals. Our data show that diets containing native starch increase the abundance of Lactobacillus in the gut microbiome, while those containing plant-derived fiber mainly enrich the level of Clostridium Greater numbers of Fusobacteria and Proteobacteria are detected in carnivorous birds, while in birds fed a commercial corn-soybean basal diet, a stronger inner-connected microbial community containing Clostridia and Bacteroidia was enriched. Furthermore, the metagenome functions of the microbes (such as lipid metabolism and amino acid synthesis) were adapted to the different food types to achieve a beneficial state for the host. In conclusion, the covariation of diet and gut microbiome identified in our study demonstrates a modulation of the gut microbiome by dietary diversity and helps us better understand how birds live based on diet-microbiome-host interactions.IMPORTANCE Our study identified food source, rather than host phylogeny, as the main factor modulating the gut microbiome diversity of nonpasserine birds, after minimizing the effects of other complex interfering factors such as weather, season, and geography. Adaptive evolution of microbes to food types formed a dietary-microbiome-host interaction reciprocal state. The covariation of diet and gut microbiome, including the response of microbiota assembly to diet in structure and function, is important for health and nutrition in animals. Our findings help resolve the major modulators of gut microbiome diversity in nonpasserine birds, which had not previously been well studied. The diet-microbe interactions and cooccurrence patterns identified in our study may be of special interest for future health assessment and conservation in birds.

Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age

Background

Colonization of intestinal microbiota in ruminant during the early life is important to host health, metabolism and immunity. Accumulating evidence revealed the ameliorative effect of milk replacer administration in the gut microbial development of early-weaned ruminants. Yimeng black goats (YBGs) inhabiting Shandong, China show a complex intestinal microbial ecosystem, but studies of their gut microbiota are still insufficient to report. Here, this study was performed to investigate how the gut microbiota develops in weaned YBGs with the effect of age and milk replacer.

Results

Results indicated that both age and milk replacer were important factors to change the gut microbiota of YBGs. Although the alpha diversity of gut microbiota did not change with the age of YBGs, the taxonomic compositions significantly changed. The relative abundance of some beneficial bacteria such as Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, Eubacterium and Barnesiella significantly decreased and subsequently increase with age, which contributes to maintain the stability of intestinal environment and realize the diversity of intestinal functions. The relative abundance of Porphyromonas, Brevundimonas, Flavobacterium, Stenotrophomonas, Propionibacterium, Acinetobacter, Enterococcus and Clostridium belong to pathogenic bacteria in milk replacer-treated YBGs was significantly decreased. Additionally, some beneficial bacteria such as Ruminococcus, Ruminococcaceae, Christensenellaceae and Ruminiclostridium also display a trend of decreasing first followed by gradually increasing.

Conclusions

This study first revealed the gut bacterial community alterations in YBGs with the effect of age and milk replacer. This study also characterized the gut microbial distribution in YBGs with different ages and provided better insight into microbial population structure and diversity of YBGs. Moreover, milk replacer may serve as a good applicant for improving gut microbial development in early-weaned YBGs.

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

Background

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

Results

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

Conclusions

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

The fungicide thiram perturbs gut microbiota community and causes lipid metabolism disorder in chickens

Fungicide thiram, a representative dithiocarbamate pesticide can cause potential health hazards to humans and animal health due to the residues in various agricultural products. However, the effects of thiram on lipid metabolism by perturbing gut microbiota of chickens are not clear. Our study was aimed to explore the protective of polysaccharide extracted from Morinda officinalis (MOP) on acute thiram-exposed chickens, and to analyze the association between alteration of gut microbiota and lipid metabolism. Three hundred chicks are fed with a normal diet, thiram-treated diet (100 mg/kg), and a thiram-treated diet supplemented with 250, 500, or 1000 mg/kg MOP was used in this study, respectively. The results showed that thiram exposure prominently elevated liver index, changed liver function by histopathological examination and serum biochemistry diagnoses, and increased blood lipid parameters. Meanwhile, the expression level of some key genes in hepatic lipid metabolism dysregulated significantly in the thiram-exposed chickens. Furthermore, 16S rRNA gene sequencing indicated that thiram exposure can significantly alter the richness, diversity, and composition of the broiler fecal microbiota, and the relative abundance of Firmicutes and Proteobacteria was also affected at the phylum level. In addition, some microbial populations including Lactobacillus, Ruminococcus, Oscillospira, Blautia, and Butyricicoccus significantly decreased at the genus level, whereas the Klebsiella was opposite. Correlation analysis further revealed a significant association between microorganisms and lipid metabolism-related parameters. Optimistically, 500 mg/kg MOP can alleviate the damage of thiram in the gut and liver. Together, these data suggest that thiram exposure causes the imbalance of the gut microbiota and hepatic lipid metabolism disorder in chickens.

Milk Replacer Supplementation Ameliorates Growth Performance and Rumen Microbiota of Early-Weaning Yimeng Black Goats

Increasing evidence has indicated the ameliorative effect of milk replacer supplementation in ruminants for regulating their early growth and rumen development. However, it is still unclear whether milk replacer supplementation has a beneficial role in the growth performance and rumen microbiota of Yimeng black goats (YBGs). Therefore, this study was performed to investigate the effects of milk replacer on growth performance and rumen microbiota of YBGs. Our results revealed that milk replacer supplementation could significantly improve the growth performance of YBGs. Additionally, the results of alpha and beta diversities indicated that there was no significant difference in richness and diversity between the control and milk replacer-treated YBGs. At the phylum level, Bacteroidetes, Firmicutes, and Proteobacteria were the most dominant phyla in all the samples at different stages. Moreover, the YBGs treated with milk replacer possessed a higher abundance of Verrucomicrobia than that in the control YBGs, while the level of Actinobacteria was obviously decreased. It is noteworthy that the abundance of Proteobacteria in the control YBGs was higher than that in the YBGs supplemented with milk replacer throughout the experiment. At the level of genus, the differences in the richness between control and milk replacer supplement YBGs were gradually observed. Compared with the control YBGs, the proportion of Akkermansia, Veillonella, Anaerovibrio, Ruminococcaceae_NK4A214_group, Ruminococcus_1, and Ruminococcus_2 was increased in the YBGs treated with milk replacer, whereas Turicibacter was decreased. In conclusion, milk replacer supplementation may serve as a good applicant for ameliorating early YBGs development and rumen microbiota.

Microbial Community and Short-Chain Fatty Acid Mapping in the Intestinal Tract of Quail

Simple Summary

Quail is an economically important type of poultry, valued for its high meat quality and abundant egg nutrition. It is also an important laboratory research animal, widely used in developmental biology and toxicology tests. Since the gut microbiota plays a vital role in the host’s growth and health, we investigated the microbiota inhabiting the duodenum, jejunum, ileum, cecum, and colorectum of quail in the present study, using 16S rRNA gene sequencing and qPCR. The concentrations of short-chain fatty acids (SCFAs) were evaluated using gas chromatography. We found that the microbiota in the cecum was different from other intestinal sections and the enriched inhabitants of SCFA-producing bacterial genera made cecum the core locations of SCFA production in quail. The results of this study will provide fundamental data for further quail microbiology and functional studies.

Abstract

Quail is raised throughout China for egg and meat production. To deeply understand the gastrointestinal microbial composition and metabolites of quail, the present study characterized the microbiota inhabiting five intestinal locations of eight-week-old quail using 16S rRNA gene sequencing and qPCR, and evaluated the concentrations of short-chain fatty acids (SCFAs) in each individual location using gas chromatography. The results showed that Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Deferribacteres were the five most abundant phyla in the intestinal tract of quail. Firmicutes was largely dominant (>95%) in the small intestine, whereas Bacteroidetes increased significantly in the cecum (19.19%) and colorectum (8.09%). At the genus level, Lactobacillus was predominant in almost all sections (>50%) except in the cecum (7.26%), where Megamonas, Faecalibacterium, and Bacteroides were dominant. qPCR data indicated that the population sizes of both the total bacteria and proportions of the Firmicutes, Bacteroidetes, and Bacteroides group increased going from the proximal toward the distal end of the intestine in quail. The SCFA-producing bacterial genera Bacteroides, Faecalibacterium, Alistipes, Blautia, Parabacteroides, and Clostridium were of higher richness in the cecum and colorectum, where, accordingly, more SCFAs were produced. These findings will be helpful for the future study of quail microbiology, as well as its relationship with productive performance and health.

Comparative analysis of microbial community structure between healthy and Aeromonas veronii-infected Yangtze finless porpoise

Background

The gut microbiota is a complex ecosystem, which is essential for the metabolism, health and immunity of host. Many diseases have been shown to be closely related to the alteration of intestinal flora. Aeromonas veronii as a conditioned pathogen can cause disease in Yangtze finless porpoise through intestinal infections. However, it is not clear whether the disease caused by Aeromonas veronii is related to changes of intestinal flora. In the current study, the diversity and composition of gut microbiota in the healthy and Aeromonas veronii-infected Yangtze finless porpoise were evaluated by high-throughput sequencing to further investigate the potential association between intestinal flora alteration and pathogen invasion.

Results

A total of 127,3276 high-quality sequences were achieved and 2465 operational taxonomic units (OTUs) were in common among all samples. The results of alpha diversity showed that there was no obvious difference in richness and diversity between healthy and Aeromonas veronii-infected Yangtze finless porpoise. Firmicutes, Bacteroidetes and Proteobacteria were the most dominant phyla in all samples. In addition, the healthy Yangtze finless porpoise exhibited higher abundance of Firmicutes and Fusobacteria than Aeromonas veronii-infected Yangtze finless porpoise, while, the level of Proteobacteria was decreased. At the genus level, Paeniclostridium and Paraclostridium were the predominant bacteria genera in the CK (healthy Yangtze finless porpoise) group. In the DIS (Aeromonas veronii-infected Yangtze finless porpoise) group, Lactobacillus and unidentified_Enterobacteriaceae were the dominant bacteria genera and the proportion of Paeniclostridium, Paraclostridium, Terrisporobacter, Cetobacterium, Candidatus Arthromitus, Terrabacter and Dechloromonas were reduced.

Conclusions

In conclusion, our results showed that Aeromonas veronii infection can alter the gut microbiota of the Yangtze finless porpoise by affecting the number of harmful bacteria and beneficial bacteria.

Biogeography of microbiome and short-chain fatty acids in the gastrointestinal tract of duck

It is generally accepted that domestic ducks are valuable protein sources for humans. The gastrointestinal ecosystem contains enormous and complicated microbes that have a profound effect on the nutrition, immunity, health, and production of domestic ducks. To deeply understand the gastrointestinal microbial composition of domestic ducks, we investigated the microbiomes of 7 different gastrointestinal locations (proventriculus, gizzard, duodenum, jejunum, ileum, cecum, and rectum) and the short-chain fatty acids in 15 healthy muscovy ducks based on 16S rRNA gene sequencing, qPCR, and gas chromatography. As a result, 1 029 735 sequences were identified into 35 phyla and 359 genera. Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria were the major phyla, with Bacteroidetes being most abundant in the cecum. The population of the total bacteria and the representatives of the Firmicutes, Bacteroidetes, and Bacteroides groups increased from the proximal to the distal part of the GIT. Bacteroides was the most dominant group in the cecum. Acetate, propionate, and butytrate, as well as gene copies of butyryl-CoA including acetate-CoA transferase and butyrate kinase, were significantly higher in cecum than in other sections. Isobutyrate, valerate, and isovalerate were only found in the cecum. The differences of microbial composition and the short-chain fatty acids of their metabolites among these 7 intestinal locations might be correlated with differences in gut function. All these results provide a reference for the duck gastrointestinal microbiome and a foundation for understanding the types of bacteria that promote health and enhance growth performance and decrease instances of disease in duck breeding.

Spatial heterogeneity of the shorebird gastrointestinal microbiome

The gastrointestinal tract (GIT) consists of connected structures that vary in function and physiology, and different GIT sections potentially provide different habitats for microorganisms. Birds possess unique GIT structures, including the oesophagus, proventriculus, gizzard, small intestine, caeca and large intestine. To understand birds as hosts of microbial ecosystems, we characterized the microbial communities in six sections of the GIT of two shorebird species, the Dunlin and Semipalmated Sandpiper, identified potential host species effects on the GIT microbiome and used microbial source tracking to determine microbial origin throughout the GIT. The upper three GIT sections had higher alpha diversity and genus richness compared to the lower sections, and microbial communities in the upper GIT showed no clustering. The proventriculus and gizzard microbiomes primarily originated from upstream sections, while the majority of the large intestine microbiome originated from the caeca. The heterogeneity of the GIT sections shown in our study urges caution in equating data from faeces or a single GIT component to the entire GIT microbiome but confirms that ecologically similar species may share many attributes in GIT microbiomes.

Optimization extraction and characterization of Artemisia ordosica polysaccharide and its beneficial effects on antioxidant function and gut microbiota in rats

In this study, a novel polysaccharide was isolated from Artemisia ordosica by water-extraction-ethanol-precipitation method. The optimal extraction conditions of Artemisia ordosica polysaccharide (AOP) were determined by single factor investigation and response surface methodology optimization, and were shown as follows: a liquid–solid ratio of 15.4 : 1 mL g⁻¹, extraction time of 4.3 h, extraction temperature of 60 °C. Under the optimal conditions, the extraction yield and the sugar content of the AOP were 5.56% and 52.65%. Gel permeation chromatography coupled to multi-angle laser light scattering, a refractive index detection system and ion-exchange chromatography were used to determine the characterization of AOP. These results indicated that AOP, with a molecular weight of 2.1 kDa (62.6%) and 1.5 kDa (37.4%), had narrow polydispersity and rod conformations, and was composed of arabinose, galactose, glucose, xylose, mannose, galacturonic acid and glucuronic acid with molar ratio of 6.87 : 10.67 : 54.13 : 2.49 : 18.37 : 4.83 : 2.64 : 2.64. In addition, AOP exerted antioxidant ability in vitro and in vivo (rats). Moreover, AOP significantly modulated the composition of cecal microbiota population. Therefore, AOP is expected to be a functional ingredient for health improvement through improving antioxidant ability and modulating gut health.

Artemisia ordosica polysaccharide is expected to be functional ingredient for health improvement through improving antioxidant ability and modulating gut health.

Characterization of the microbiome along the gastrointestinal tracts of semi-artificially reared bar-headed geese (Anser indicus)

As one of the dominant waterfowl species of wetland areas in the Qinghai-Tibet Plateau, since 2003, artificial rearing of bar-headed geese (Anser indicus) has increased in several provinces of China for the purpose of conservation and economic development. In this study, we systematically characterized the microbial community diversity, compositions and predicted functions of semi-artificially reared bar-headed geese by sampling five different gut locations (the oropharynxs, crops, gizzards, ceca, and cloacae) along the gastrointestinal tracts of three individuals. Alpha diversity analyses showed that the gizzards had the richest species diversity and that the ceca had the least. Beta diversity analyses showed that the cecal samples formed their own cluster, while samples from the oropharynxs, crops, gizzards, and cloacae overlapped with each other. At the phylum level, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria constituted the top five dominant phyla among all five gastrointestinal sections. At the genus level, a total of 10 genera with proportions above 2.5% were found to be significantly different among the gastrointestinal sections. Furthermore, 53 genera were detected in all gastrointestinal sections of bar-headed geese. PICRUSt data also predicted a group of microbial functions overrepresented in the different segments of the gastrointestinal tracts. Understanding the microbiota along the bar-headed geese gastrointestinal tracts is essential for future microbiological study of this bird and may contribute to the development of geese husbandry.

Probiotic potential of Lactobacillus on the intestinal microflora against Escherichia coli induced mice model through high-throughput sequencing

The aim of this study was to evaluate the antibacterial potential of Lactobacillus screened from Tibetan yaks on clinical symptoms and intestinal microflora in enteroinvasive Escherichia coli (EIEC) induced mice model. In vitro study, Lactobacillus reuteri (LR1) exhibited stronger resistance to acid and bile and inhibited the growth of EIEC than Lactobacillus mucosae (LM1). The mice were randomly divided into four groups i.e. the LR1 group (LR1 1 × 10⁹ CFU/day), LM1 group (LM1 1 × 10⁹ CFU/day), blank control group and control group. Mice in control, LR1, and LM1 groups were challenged with EIEC on day 23. The body weight in the control and LM1 groups were significantly decreased after the infection with EIEC (P < 0.05), whereas the body weight of mice in the LR1 group did not change significantly (P > 0.05). The lowest diarrhea rate was recorded in the LR1 group after infection with EIEC. The results showed that the number of pathogens in the control group was higher than that in the experimental groups. The sequence analysis and OTU classification showed that the duodenum, ileum, and cecum of mice in the LR1 group had the highest number of OTUs compared with other groups. Whereas, the diversity analysis showed that in duodenum, ileum and cecum of mice in the LR1 group had the highest abundance and diversity. The composition of intestinal microbes indicated the presence of high proportions of Firmicutes, Proteobacteria and Bacteroidetes. Heat map analysis indicated high abundance of Bdello vibrio in the duodenum of mice in the LR1 group, while many pathogens were found in the different part of intestines in the control group, such as Streptococcus, Clostridium and Pseudomonas. In conclusion, pre-supplementation of LR1 alleviate the clinical symptoms caused by E. coli, and promote a healthy gut flora.

Bacillus subtilis Strain DSM 29784 Modulates the Cecal Microbiome, Concentration of Short-Chain Fatty Acids, and Apparent Retention of Dietary Components in Shaver White Chickens during Grower, Developer, and Laying Phases

This study investigated the efficacy of a single strain of Bacillus subtilis (SSB) in modulating the composition of cecal microbiota and its link to the concentration of short-chain fatty acids (SCFA) and apparent retention (AR) of components. A total of 720, 4-week-old Shaver White chicks were allotted to control (CON), 1.1E+08 (low, LSSB), 2.2E+08 (medium, MSSB), or 1.1E+09 (high, HSSB) CFU/kg of diet groups. At grower (10-week), developer (16-week), and laying (28-week) phases, excreta and cecal digesta samples were taken for AR, microbial, and SCFA analyses. Microbial analysis involved high-throughput sequencing of the V3-V4 hypervariable regions of 16S rRNA gene. Bacterial diversity decreased (P < 0.05) at the developer phase as the SSB dose increased; however, a distinct clustering pattern (P < 0.05) of bacterial community was noted. Bacteroides and Faecalibacterium were differentially enriched in the developer for SSB-fed compared to CON-fed birds. Although no differences in microbial diversity were detected in grower and layer phases, different species of Clostridium (XVIII, XIVa, IV, and XIVb)-major butyrate producers-were identified in all phases, with stronger effect sizes for SSB-fed compared to CON-fed birds. Isobutyric acid was elevated in dose response (P = 0.034) in layer phase. In addition, the relative abundances of Alistipes, Lactobacillus, and Bifidobacterium were positively correlated (P < 0.05), with AR of most components for SSB-fed birds in the pullet phase. The results suggested that supplementing chickens' diet with B. subtilis DSM 29784 may selectively enrich beneficial bacterial communities, which in turn are critical in promoting the growth and performance of hens.IMPORTANCE In egg-laying chickens, the trend in the move away from the cage to alternative housing systems and restriction in antimicrobial use requires alternative approaches to maintain health and prevent diseases. There is increased research and commercial interest toward alternative gut health solutions while improving the performance and product safety in poultry production systems. One such approach, in recognition of the importance of the gut microbial community, is the use of microbes as feed supplements (such as probiotics). Unlike meat-type chickens, studies assessing the efficacy of such microbial supplements are limited for egg-laying chickens. Thus, by conducting a comprehensive assessment of the hen microbiota in response to various levels of B. subtilis DSM 29784 during the pullet phase (grower and developer) and the layer phase, the present study demonstrates the importance of direct-fed microbes in modulating gut microbiome, which may relate to improved performance efficiency in the pullet and layer phases.

Composition, diversity and function of gastrointestinal microbiota in wild red-billed choughs (Pyrrhocorax pyrrhocorax)

Hitherto, virtually nothing is known about the microbial communities related to the bird species in the family Corvidae. To fill this gap, the present study was conducted to provide a baseline description of the gut microbiota of wild red-billed choughs (Pyrrhocorax pyrrhocorax). In this study, microbiota from four gastrointestinal locations (oropharynx, gizzard, small intestine, and large intestine) of three wild red-billed choughs were analyzed using the Illumina MiSeq sequencing platform by targeting the V4-V5 regions of the 16S rRNA genes. The gut microbiota of the red-billed choughs were dominated by the phylum Firmicutes (59.56%), followed by Proteobacteria (16.56%), Bacteroidetes (13.86%), and Actinobacteria (7.03%), which were commonly detected in avian gut ecosystems. Genus-level compositions were found to be largely dominated by Lactobacillus (18.21%), Weissella (12.37%), Erysipelatoclostridium (6.94%), Bacteroides (6.63%), Escherichia-Shigella (5.15%), Leuconostoc (4.60%), Proteus (3.33%), Carnobacterium (2.71%), Lactococcus (1.69%), and Enterococcus (1.63%). The overall intestinal microbiota was enriched with functions related to ATP-binding cassette (ABC) transporters, DNA repair and recombination proteins, purine metabolism, ribosome, transcription factors, pyrimidine metabolism, peptidases, and two-component system. In terms of four different gastrointestinal locations, hierarchical clustering analysis and principal coordinate analysis showed that microbial communities of the oropharynx, gizzard, small intestine, and large intestine formed four separated clusters. A total of 825 OTUs and 382 genera were detected in all four gastrointestinal locations, which were considered as the major microbes in the intestines of red-billed choughs. Coexistence of lactic acid bacteria and potential pathogens in the gut environments of red-billed choughs required further investigations.

Comparison of the Intestinal Microbial Community in Ducks Reared Differently through High-Throughput Sequencing

Birds are an important source of fecal contamination in environment. Many of diseases are spread through water contamination caused by poultry droppings. A study was conducted to compare the intestinal microbial structure of Shaoxing ducks with and without water. Thirty 1-day-old Shaoxing ducks (Qingke No. 3) were randomly divided into two groups; one group had free access to water (CC), while the other one was restricted from water (CT). After 8 months of breeding, caecal samples of 10 birds from each group were obtained on ice for high-throughput sequencing. A total of 1507978 valid sequences were examined and clustered into 1815 operational taxonomic units (OTUs). At phylum level, Firmicutes (41.37%), Bacteroidetes (33.26%), Proteobacteria (13.67%), and Actinobacteria (8.26%) were found to dominate the microbial community in CC birds, while Firmicutes (53.62%), Bacteroidetes (33.06%), and Actinobacteria (11.13%) were uncovered to be the prime phyla in CT ducks. At genus level, Bacteroides (25.02%), Escherichia-Shigella (11.02%), Peptococcus (7.73%) and Parabacteroides (5.86%) were revealed to be the mainly genera in the CC group ducks, while Bacteroides (18.11%), Erysipelatoclostridium (10.94%), Ruminococcaceae_unclassified (10.43%), Lachnospiraceae_unclassified (5.26%), Coriobacteriales_unclassified (5.89%), and Faecalibacterium (4.2%) were detected to staple the microbial flora in the CT birds. One phylum and 13 genera were found to have the significant difference between the two bird groups (p<0.05). At phylum level, Proteobacteria in CT ducks were found to be obviously lower than ducks in CC birds (p<0.05). At genus level, Escherichia-Shigella (p<0.05) and Peptococcus (p<0.05) were found to be notably lower in CT birds, while Erysipelatoclostridium (p<0.05), Ruminococcaceae_unclassified (p<0.01), Coriobacteriales_unclassified (p<0.05), Faecalibacterium (p<0.01), Atopobiaceae_unclassified (p<0.01), Alistipes (p<0.05), Eggerthellaceae_unclassified (p<0.05), Prevotella_7 (<0.05), Rikenellaceae_RC9_gut_group (p<0.05), Prevotellaceae_uncultured (p<0.05), and Shuttleworthia (p<0.05) were observed to be prominently higher in CT ducks. In conclusion, the present study revealed the effects of keeping ducks away from swimming with obvious changes in the microbial community. Though higher microbial richness was found in the ducks without swimming, more pathogenic genera including Eggerthella, Erysipelatoclostridium, Alistipes, Prevotella_7, and Shuttleworthia; zoonotic genera including Eggerthella and Shuttleworthia; inflammatory genus Alistipes; anti-inflammatory Faecalibacterium genus; and tumor genus Rikenellaceae were examined in these ducks. The CT ducks also showed significant changes at genera level regarding the metabolism (Peptococcus, Ruminococcaceae, and Coriobacteriales).

Intestinal Morphologic and Microbiota Responses to Dietary Bacillus spp. in a Broiler Chicken Model

Dietary inclusion of probiotic Bacillus spp. beneficially affect the broiler chickens by balancing the properties of the indigenous microbiota causing better growth performance. The effects of three Bacillus spp. on the growth performance, intestinal morphology and the compositions of jejunal microflora were investigated in broiler chickens. A total of 480 1-day-old male Arbor Acres broilers were randomly divided into four groups. All groups had six replicates and 20 birds were included in each replicate. The control birds were fed with a corn-soybean basal diet, while three treatment diets were supplemented with Bacillus coagulans TBC169, B. subtilis PB6, and B. subtilis DSM32315 with a dosage of 1 × 109 cfu/kg, respectively. The experiment lasted for 42 days. The compositions and diversity of jejunal microflora were analyzed by MiSeq high-throughput sequencing. The B. coagulans TBC169 group showed marked improvements of growth performance, nutrient digestibility and intestinal morphology compared with the other B. subtilis treatments. B. coagulans TBC169 supplementation improved the average body weight (BW), average daily weight gain (ADG), total tract apparent digestibility of crude protein and gross energy (GE), and reduced feed conversion rate (FCR) compared with the control group (P < 0.05). The villus height to crypt depth ratio (VH/CD) of jejunum and duodenum was increased in the birds fed with B. coagulans TBC169 compared with the control group (P < 0.05). However, two B. subtilis treatments presented more positive variation of the jejunum microflora of chickens than that in the B. coagulans TBC169 group. B. subtilis PB6 and B. subtilis DSM32315 treatments improved the diversity of jejunal microbiota on day 21 compared with the control (P < 0.05), while which were decreased on day 42 (P < 0.05). The supplementation with B. coagulans TBC169 significantly improved the proportion of Firmicutes, otherwise two B. subtilis significantly improved the proportion of Proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria at the phylum level during starter phase and decreased the proportion of Bacteroidetes during growing phase compared with the control. The supplementation with B.subtilis DSM32315 significantly improved the proportion of Clostridiales during starter phase, whereas two B. subtilis significantly improved the proportion of Pseudomonas, Burkholderia, Prevotella, DA101 during growing phase at the genus level compared with the control. In conclusion, the dietary supplementation with probiotic Bacillus spp. strains improved body weight and intestinal morphology in broiler chickens, which might be associated with the gut microbiota.

Polygonatum odoratum Polysaccharides Modulate Gut Microbiota and Mitigate Experimentally Induced Obesity in Rats

Increasing evidence suggests that the gut microbiota plays vital roles in metabolic diseases. Polygonatum odoratum extract alleviates hyperglycemia and hyperlipidemia, but the underlying mechanism remains unclear. This study investigated the effects of P. odoratum polysaccharides (POPs) on high-fat diet (HFD)-induced obesity in rats and whether these effects were related to modulation of gut microbiota. POP treatment attenuated weight gain, fat accumulation, epididymal adipocyte size, liver triglycerides, and total liver cholesterol content in HFD-fed rats. POP administration also increased short-chain fatty acids (SCFAs), including isobutyric acid, butyric acid, and valeric acid. POP upregulated the expression of genes involved in adipocyte differentiation (Pparg, Cebpa, Cebpb) and lipolysis (Ppara, Atgl), and downregulated those related to lipid synthesis (Srebpf1, Fabp4, Fas), with corresponding changes in PPARγ and FABP4 protein expression. Finally, POP enhanced species richness and improved the gut microbiota community structure, reducing the relative abundances of Clostridium, Enterococcus, Coprobacillus, Lactococcus, and Sutterella. Principal coordinates analysis (PCoA) revealed a clear separation between HFD-fed rats and all other treatment groups. Correlation analysis identified negative and positive associations between obesity phenotypes and 28 POP-influenced operational taxonomic units (OTUs), including putative SCFA-producing bacteria. Our data suggest that POP supplementation may attenuate features of obesity in HFD-fed rats in association with the modulation of gut microbiota.

Comparative analysis of gut microbial community in healthy and tibial dyschondroplasia affected chickens by high throughput sequencing

Tibial dyschondroplasia (TD) is a common skeletal problem of avian species. The cause and etiology of this disorder is still not clear. The intestinal bacterial community is a complex ecosystem and plays very important role in healthy life of human and animals. Many researchers have made the connection between diseases and alteration of gut microbiota. However, little is know about the role of gut microbiota in TD. The objective of this study was to explore the diversity and composition of small and large intestinal bacterial communities of TD chickens. The intestinal contests were collected from healthy and TD chickens at day 18 of the trail. The V3-V4 region of 16S rDNA was amplified and sequenced by high-throughput sequencing. Our results indicated that healthy chickens had higher abundance and diversity of gut microbiota than TD chickens but there was no significant difference (P > 0.05) among the gut microbiota of small and large intestine. However, the composition of bacterial communities were significantly different (P < 0.05) between healthy and TD chickens. The occurrence of gut pathogens associated with immunity and inflammation were much higher in the intestinal contests of TD chickens as compared to healthy ones. In summary, our results showed an interesting difference of gut microbiota between healthy and TD chickens, which provided a new thought about the pathogenesis of TD.