Microbial diversity within the digestive tract contents of Dezhou donkeys

Rectal microbiomes and serum metabolomics reveal the improved effect of Artemisia ordosica crude polysaccharides on the lactation performance, antioxidant and immune responses of lactating donkeys

This study is aimed at investigating the effects of dietary supplementation with Artemisia ordosica crude polysaccharides (AOCP) on lactation performance, antioxidant status, and immune status of lactating donkeys and analyzing rectal microbiomes and serum metabolomes. Fourteen lactating Dezhou donkeys with similar age (6.16 ± 0.67 years of BW ± SD), weight (250.06 ± 25.18 kg), days in milk (39.11 ± 7.42 d), and averaged parity of 3 were randomly allocated into 2 treatments: a control group (CON, basal diet) and an AOCP group (AOCP, basal diet with 1.0 g/kg DM AOCP). Ten weeks were allotted for the experiment, 2 weeks for adaptation, and 8 weeks for collecting data and samples. The results showed that supplementation of donkey diets with AOCP increased lactation performance, including dry matter intake, milking yield, estimated milk yield, solids-corrected milk, energy-corrected milk, milk fat yield, milk protein yield, milk lactose yield, milk total solids yield, and milk solid not fat yield. The digestibility of dry matter, crude protein, acid detergent fiber, and neutral detergent fiber was increased in the AOCP group compared with the CON group. The AOCP group increased the concentrations of immunoglobulin A, immunoglobulin G, and immunoglobulin M, the activities of the superoxide dismutase, catalase and total antioxidant capacity in the serum. AOCP decreased the concentrations of tumor necrosis factor-α, nitric oxide, reactive oxygen species, and malondialdehyde in the serum. Compared with the CON group, AOCP increased propionate, butyrate, isovalerate, and total VFA concentrations in rectal feces (P < 0.05). The addition of AOCP to increased diversity (Shannon index) and altered structure of the rectal microflora. As a result of AOCP supplementation, there has been a significant improvement in the colonization of beneficial bacteria, including Lactobacillus, Unclassified_f_Prevotellacea, Ruminococcus, and Fibrobacter genera. In contrast, a decrease in the colonization of the Clostridium_sensu_stricto_1 bacterial genus and other pathogenic bacteria was observed. Meanwhile, metabolomics analysis found that AOCP supplementation upregulated metabolites L-tyrosine content while downregulating 9(S)-HODE, choline, sucrose, LysoPC (18:0), LysoPC (18:1(9Z), and LysoPC (20:2(11Z,14Z)) concentrations. These altered metabolites were involved in the PPAR signaling pathway, prolactin signaling pathway, glycerophospholipid metabolism, carbohydrate digestion and absorption, and tyrosine metabolism pathways, which were mainly related to antioxidant capacity, immune responses, and protein metabolism in the lactating donkeys. As a consequence of feeding AOCP diets, beneficial bacteria were abundant, and antioxidant and protein metabolism-related pathways were enriched, which may enhance lactation performance in donkeys. Therefore, supplementing AOCP diets is a desirable dietary strategy to improve donkey health and lactation performance.

Identification of Dezhou donkey muscle development-related genes and long non-coding RNA based on differential expression analysis

Long non-coding RNAs (lncRNAs) play a critical role in the development of muscles. However, the role of lncRNAs in regulating skeletal muscle development has not been studied systematically in the donkey. In this study, we performed the RNA sequencing for different stages of muscles in donkeys, and investigate their expression profile, which showed that 3215 mRNAs (p-adjust <0.05) and 471 lncRNAs (p-value <0.05) were significantly differently expressed (DE) verified by RT-qPCR. GO and KEGG enrichment analysis indicated that DE genes and target genes of DE lncRNAs were associated with muscle development in the donkey. We also found these four target genes (DCN, ITM2A, MUSTN1, ARRDC2) involved in skeletal muscle growth and development. Combined with transcriptome data, network, and RT-qPCR results showed that four co-expression networks of DCN and lnc-008278, ITM2A and lnc_017247, MUSTN1 and lnc_030153, and ARRDC2 and lnc_033914, which may play an important role in the formation and development of muscle in the donkey.

Single nucleotide polymorphisms (SNPs) and indels identified from whole-genome re-sequencing of four Chinese donkey breeds

This paper represents the fundamental report of the survey of genome-wide changes of four Chinese indigenous donkey breeds, Dezhou (DZ), Guangling (GL), North China (NC), and Shandong Little donkey (SDL), and the findings will prove usefully for identification of biomarkers that perhaps predict or characterize the growth and coat color patterns. Three genomic regions in CYP3A12, TUBGCP5, and GSTA1 genes, were identified as putative selective sweeps in all researched donkey populations. The loci of candidate genes that may have contributed to the phenotypes in body size (ACSL4, MSI2, ADRA1B, and CDKL5) and coat color patterns (KITLG and TBX3) in donkey populations would be found in underlying strong selection signatures when compared between large and small donkey types, and between different coat colors. The results of the phylogenetic analysis, FST, and principal component analysis (PCA) supported that each population cannot clearly deviate from each other, showing no obvious population structure. We can conclude from the population history that the formation processes between DZS and NC, GL, and SDL are completely different. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Chinese donkey breeding programs.

Effects of Concentrate Feeding Sequence on Growth Performance, Nutrient Digestibility, VFA Production, and Fecal Microbiota of Weaned Donkeys

In this study, effects on the growth performance, nutrient digestibility, volatile fatty acids (VFA) production, and fecal microbiota of weaned donkeys were observed using different concentrate feeding sequences. Fifteen healthy 6-month-old weaned male donkeys with a body weight of 117.13 ± 10.60 kg were randomly divided into three treatment groups, including group C1 (roughage-then-concentrate), group C2 (concentrate-then-roughage), and group C3 (total mixed ration, TMR). The experiment lasted 35 d. We measured nutrient digestion by the acid-insoluble ash method and analyzed the fecal microbiota of the weaned donkeys by high-throughput sequencing of 16s rRNA genes in the V3-V4 region. The results show that group C3 obtained the best growth performance, and the digestibility of crude protein (CP) and crude extract (EE) was significantly higher than that of group C1 (p < 0.05). Acetic acid, isobutyric acid, valeric acid, isovaleric acid, and caproic acid were notably different among all groups (p < 0.05). In addition, we observed that Firmicutes and Bacteroidetes were dominant in the fecal microbes of each group, and Firmicutes was significantly higher in group C3 (p < 0.05). At the genus level, the different genera were Treponema, Rikenellaceae-RC9-gut-group, Unidentified-F082, and Bacteroidales-RF16-group (p < 0.05). The prediction of fecal microbiota function by PICRUSt indicated that different feeding sequences had minimal impact on the function of the fecal microbiota, particularly on the high-abundance pathway. In summary, the concentrate feeding sequence changed the composition of the fecal microbe of weaned donkeys.

Comparative analysis of intestinal flora between rare wild red-crowned crane and white-naped crane

Introduction

Animal intestines are extremely rich in microbial ecosystems. Numerous studies in different fields, such as epidemiology and histology, have revealed that gut microorganisms considerably mediate the survival and reproduction of animals. However, gut microbiology studies of homogeneously distributed wild cranes are still rare. This study aimed to understand the structural composition of the gut microbial community of wild cranes and elucidate the potential roles of the microorganisms.

Methods

We used high-throughput sequencing to analyze the gut microbial community structure of wild cranes in the Zhalong Nature Reserve.

Results

A total of 1,965,683 valid tags and 5248 OTUs were obtained from 32 fecal samples. Twenty-six bacteria phyla and 523 genera were annotated from the intestinal tract of the red-crowned crane. Twenty-five bacteria phyla and 625 genera were annotated from the intestine of the white-naped crane. Firmicutes, Proteobacteria, and Bacteroidetes are the dominant bacterial phyla in the intestinal tract of red-crowned cranes, while Catellicoccus, Lactobacillus, Neisseria, and Streptococcus were the dominant genera. The dominant bacterial phyla in the intestinal tract of white-naped cranes were Firmicutes, Proteobacteria, Bacteroidetes, Epsilonbacteraeota, Actinobacteria, and Fusobacteria. However, the dominant genera were Catellicoccus, Lactobacillus, Neisseria, Campylobacter, Streptococcus, Anaerobiospirillum, Romboutsia, Turicibacter, Haemophilus, and Lautropia. Firmicutes had significantly higher relative abundance in the intestine of the red-crowned than white-naped cranes (P &lt; 0.05). However, the relative abundance of Actinobacteria and Bacteroidetes was significantly higher (P &lt; 0.05) in the intestines of white-naped than red-crowned cranes. The diversity of the intestinal flora between the two crane species was significantly different (P &lt; 0.05). Besides, the alpha diversity of the intestinal flora was higher for white-naped than red-crowned cranes. Eight of the 41 functional pathways differed in the gut of both crane species (P &lt; 0.05).

Discussion

Both species live in the same area and have similar feeding and behavioral characteristics. Therefore, host differences are possibly the main factors influencing the structural and functional differences in the composition of the gut microbial community. This study provides important reference data for constructing a crane gut microbial assessment system. The findings have implications for studying deeper relationships between crane gut microbes and genetics, nutrition, immunity, and disease.

Integrated multi-omics reveals novel microbe-host lipid metabolism and immune interactions in the donkey hindgut

Evidence has shown that gut microbiota play a key role in host metabolism and health; however, little is known about the microbial community in the donkey hindgut as well as the interactions that occur between gut microbes and the host. This study aimed to explore the gut microbiome differences by analyzing the microbial community and differentially expressed genes (DEGs) related to lipid metabolism and the immune system along the donkey hindgut. The hindgut tissues (cecum, ventral colon, and dorsal colon) were separated, and the contents of each section were collected from six male donkeys for multi-omics analysis. There were significant differences in terms of dominant bacteria among the three sections, especially between the cecum and dorsal colon sites. For instance, species belonging to Prevotella and Treponema were most abundant in the cecum, while the Clostridiales_bacterium, Streptococcus_equinus, Ruminococcaceae_bacterium, etc., were more abundant in the dorsal colon. Apart from propionate, the concentrations of acetate, isobutyrate, valerate and isovalerate were all lower in the cecum than in the dorsal colon (p < 0.05). Furthermore, we identified some interesting DEGs related to lipid metabolism (e.g., ME1, MBOAT1, ACOX1, ACOX2 and LIPH) and the immune system (e.g., MUC3B, mucin-2-like, IL17RC, IL1R2, IL33, C1QA, and MMP9) between the cecum and dorsal colon and found that the PPAR pathway was mainly enriched in the cecum. Finally, we found a complex relationship between the gut microbiome and gene expression, especially with respect to the immune system, and combined with protein-protein interaction (PPI) data, suggesting that the PPAR pathway might be responsible, at least in part, for the role of the hindgut microbiota in the donkeys' gut homeostasis. Our data provide an in-depth understanding of the interaction between the microbiota and function in the healthy equine hindgut and may also provide guidance for improving animal performance metrics (such as product quality) and equine welfare.

Comparison of gut microflora of donkeys in high and low altitude areas

Donkeys’ gut microbe is critical for their health and adaptation to the environment. Little research has been conducted on the donkey gut microbiome compared with other domestic animals. The Tibetan Plateau is an extreme environment. In this study, 6 Qinghai donkeys (QH) from the Tibetan Plateau and 6 Dezhou donkeys (DZ) were investigated, and the contents of 4 parts—stomach, small intestine, cecum, and rectum—were collected. 16S rRNA sequencing and metagenomic sequencing were used to analyze the composition and diversity of gut microbial communities in donkeys. The results showed that the flora diversity and richness of the hindgut were significantly higher than those of the foregut (p < 0.01), with no sex differences, and the community structure and composition of the same or adjacent regions (stomach, small intestine, cecum, and rectum) were similar. Besides, the flora diversity and richness of QH on the Tibetan Plateau were significantly higher than those of DZ (p < 0.05). The major pathways associated with QH were signal transduction mechanisms and carbohydrate transport and metabolism, and Bacteroidales were the major contributors to these functions. Our study provides novel insights into the contribution of microbiomes to the adaptive evolution of donkeys.

Dynamic alterations in the donkey fecal bacteria community and metabolome characteristics during gestation

In donkeys, the gestation period is a dynamic and precisely coordinated process involving systemic and local alterations. Both the gut microbiota and its link with blood metabolites are thought to play significant roles in maintaining maternal health and supporting fetal development during the gestation period. This study was conducted to evaluate gut microbiota changes and the correlation with plasma metabolites in Dezhou donkeys during the gestation period. The donkeys were divided into the four following groups according to their pregnancy stages: the non-pregnant (NP), early stage of pregnancy (P1), middle stage of pregnancy (P2), and late stage of pregnancy (P3) groups. A total of 24 (n = 6 per group) samples of donkey feces and plasma were collected. The results showed that the diversity (Shannon index) of fecal bacteria significantly increased throughout the gestation period. The phyla Spirochaetota and Fibrobacterota varied significantly according to the stages of pregnancy (p &lt; 0.05). At the genus level, the abundance of Treponema in pregnant donkeys was greater than that in non-pregnant donkeys (p &lt; 0.05), and the genus Streptococcus reached its maximum abundance in the P2 period (p &lt; 0.05). The abundance of Ruminococcaceae_NK4A214_group and norank_f_norank_o_WCHB1-41 linearly increased with the progression of pregnancy (p &lt; 0.05). In addition, the host plasma metabolome was altered significantly during the gestation period. Testolic acid, estradiol-17beta 3-sulfate, equol 7’-o-glucuronide, equol 4’-o-glucuronide, estrone, estrone 3-glucuronide, and estradiol were the most significant differential enriched metabolites, and they increased gradually as gestation progressed. The altered metabolites were mainly enriched in pathways matched to bile secretion, ABC transporters, amino acid metabolism, protein digestion and absorption, mineral absorption, fatty acid degradation, glycerophospholipid metabolism, and steroid hormone biosynthesis. We also found a significant correlation between the shifts in donkey fecal bacteria and changes in the host metabolism. In summary, this study provided systematic data on the fecal bacterial changes and host plasma metabolism of donkeys throughout pregnancy. The results indicated that host–bacteria interactions during the gestation period influence the host metabolism. These interactions benefit the pregnant donkeys by providing a sufficient supply of nutrients and energy for fetal growth and maternal health.

Could Weaning Remodel the Oral Microbiota Composition in Donkeys? An Exploratory Study

As the initiation point of digestion, the oral microbiome is important in maintaining oral and systemic health. However, the composition of oral microbial communities and the influence of weaning on the oral microbiota of donkey foals remains poorly characterized. The present study used buccal swab samples to determine the changes in oral microbial communities occurring at the time of weaning. A total of 20 oral swab samples were collected from two groups: preweaning donkey foals (PreW group, n = 10) and postweaning donkey foals (PostW group, n = 10). The donkey oral microbiome was analyzed by 16S rRNA gene sequencing using Illumina MiSeq. This study is the first report of the donkey oral microbiome in association with weaning. Compared to the preweaning donkeys, the oral bacteria diversity in the postweaning donkeys was increased, with a higher Simpson index. Changes in the composition of the oral microbiota between the PreW and PostW groups were observed in the present study. At the phylum level, the relative abundance of Firmicutes and Myxococcota was significantly greater in the PostW than in the PreW group. At the genus level, the Gemella, unclassified_o__Lactobacillales, and Lactobacillus were increased in the postweaning donkeys. The donkeys’ oral microbial functions were predicted using PICRUSt, and the functions related to carbohydrate metabolic pathways were significantly enriched in the oral microbiome in the PostW donkeys. In summary, the current study provides a deeper insight into the oral microbiota changes during the weaning period, and the influence of weaning together with the documented changes in diversity and composition will help us to obtain a better understanding of their long-term health impact within the oral cavities of donkey foals. However, a major limitation of the present study was that the samples were obtained from different animals in the PreW and PostW groups, which may have resulted in variability among the different individuals. Further investigation is needed to monitor the shift in oral microbes in the same individuals during the weaning period.

Plant cell wall breakdown by hindgut microorganisms: can we get scientific insights from rumen microorganisms?

Equines and ruminants have evolved as grazing herbivores with specialized gastrointestinal tracts capable of utilizing a wide range of fibrous feeds. In China, agricultural by-products, including corn straw, wheat straw, peanut vine, wheat husk, rice husk, and grass hay, have been extensively included in both equine and ruminant diets. These plant materials, which are composed predominantly of cellulose, hemicellulose, noncellulosic polysaccharides, and lignin, are largely undegradable by equines and ruminants themselves. Their breakdown is accomplished by communities of resident microorganisms that live in symbiotic or mutualistic associations with the host. Information relating to microbial composition in the hindgut and rumen has become increasingly available. Rumen fermentation is unique in that plant cell wall breakdown relies on the cooperation between microorganisms that produce fibrolytic enzymes and that ruminant animals provide an anaerobic fermentation chamber. Similar to the rumen, the equine hindgut is also an immensely enlarged fermentative chamber that includes an extremely abundant and highly complex community of microorganisms. However, few studies have characterized the microbial functions and their utilization process of lignocellulosic feeds within the equine hindgut. The process of understanding and describing plant cell wall degradation mechanisms in the equine hindgut ecosystem is important for providing information for proper feeding practices to be implemented. In the present study, we gather existing information on the rumen and equine ecosystem and provide scientific insights for understanding the process of plant cell wall breakdown within the hindgut.

Comparative Analysis of Bacterial Diversity between the Liquid Phase and Adherent Fraction within the Donkey Caeco-Colic Ecosystem

Donkey hindgut is an enlarged fermentative chamber that harbors a highly complex and extremely abundant community of anaerobic bacteria. It can be divided into two different ecological sites: liquid (Lq) phase and adherent fraction (Ad) colonized by bacteria. However, the Ad bacteria have not previously been specifically collected or directly compared with the Lq bacteria. In the present study, the digesta collected from the caecum, ventral colon and dorsal colon of nine Dezhou donkeys was separated into Lq and Ad fractions. The bacterial community structure was comparatively determined using 16S rRNA gene sequences by Illumina MiSeq. The Ad bacteria had a higher bacterial diversity than Lq bacteria due to the higher Chao and ACE index (p < 0.05). The predominant bacteria at the phylum level were Firmicutes (55.4~74.3%) and Bacteroidota (13.7~32.2%) for both the Lq and Ad fraction. The relative abundance of Bacteroidota, Spirochaetota, Fibrobacterota and Patescibacteria in the Ad fraction was greater than Lq (p < 0.05), suggesting that bacteria associated with feed particles were mainly responsible for plant fiber degradation. At the genus level, the abundance of Lactobacillus in Lq was greater than that in the Ad fraction (p < 0.05), indicating that the bacteria in the Lq fraction were better at hydrolyzing readily fermentable carbohydrates. PICRUSt showed that the activities of enzymes related to fiber degradation in the Ad fraction were also greater than Lq. In addition, the hindgut region also had a significant effect on the bacterial community composition. The relative abundance of Rikenellaceae_RC9_gut_group, Clostridium_sensu_stricto_1, Christensenellaceae_R-7_group and norank_Bacteroidales_BS11_gut_group was increased (p < 0.05) along the donkey hindgut. In summary, the present study provides evidence that bacteria adherent to plant biomass were different to those in the liquid phase within the donkey caeco-colic digesta, and bacteria associated with feed particles may mainly be responsible for plant fiber degradation.

Distribution and Difference of Gastrointestinal Flora in Sheep with Different Body Mass Index

Fat deposition is the key factor affecting the efficiency of animal husbandry production. There are many factors affecting fat deposition, in which the gastrointestinal microbiota plays an important role. Therefore, the body mass index (BMI) was introduced into the evaluation of sheep fat deposition, and the different microbiota and functional pathways of the sheep gastrointestinal tract in different BMI groups were analyzed. We selected 5% of individuals with the highest and lowest BMI from a feed test population (357 in whole group). Microorganisms in 10 sites of the gastrointestinal tract in 36 individuals (18 in each group) were evaluated by 16S rRNA V3−V4 region sequencing. There were differences (p < 0.05) in fat deposition traits between different BMI groups. In the 10 parts of the gastrointestinal tract, the diversity and richness of cecal microflora in the high-BMI group were higher than those in low-BMI Hu sheep (p < 0.05). Principal coordinate analysis (PCoA) showed that there was separation of the cecum between groups, and there were differences in the cecal microbial community. Linear discriminant analysis effect size (LEfSe) showed that most biomarkers were in the cecum. On the basis of an indepth study of cecal microorganisms, 26 different bacterial genera were obtained (p < 0.05). Correlation analysis between them and the characteristics of fat deposition in sheep showed that Colidextribacter, Alloprevotella, and Succenivibrio were positively correlated with fat deposition, while Lachnospiraceae_ND3007_Group was negatively correlated (p < 0.05). The above results show that the cecum may be an important part leading to the difference of BMI in sheep, and its microorganisms may affect the level of fat deposition.

The Fibrolytic Enzyme Profiles and the Composition of Fungal Communities in Donkey Cecum-Colon Ecosystem

Simple Summary

The donkey hindgut is a microbial-rich ecosystem in which caecum and colon fungi play an important role in dietary fiber degradation. In addition, the fibrolytic enzymes produced by hindgut microorganisms are key to the ability of equines to hydrolysis plant fiber. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. The dorsal colon presented a higher fibrolytic enzyme activity in comparison with caecum. The fungal community composition along donkey caecum and colon was determined by sequencing an internal transcribed spacer region (ITS) using Illumina MiSeq. The predominant fungi at phylum level were Ascomycota, Basidiomycota, and Neocallimastigomycota. The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum. The relative abundance of enzymes related to plant cell wall breakdown were also predicted by PICRUSt, and they were also greater in donkey colon than in caecum. The present study provided new information about fibrolytic enzyme profiles and fungal communities in donkey hindgut. The findings could therefore contribute to the further understanding of the fungal taxa and their dietary fiber degradation mechanisms in donkey hindgut ecosystem.

Abstract

The fibrolytic enzymes and the hindgut fungi in donkey cecum-colon ecosystem play an important role in dietary fiber digestion. A better understanding of the fibrolytic enzyme profiles and the fungal community along donkey caecum and colon is key for optimizing hindgut function. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. Activities of carboxymethyl cellulase, avicelase, xylanase, and acetyl esterase were greater in donkey dorsal colon than in caecum, indicating that the colon microorganisms may be more efficient in producing fibrolytic enzymes compared to caecum microbes. The fungal community composition along donkey hindgut was determined by sequencing ITS region using Illumina MiSeq. Three fungal phyla were identified by sequence comparison: Ascomycota (66.8%–74.4%), Basidiomycota (21.6%–30.9%), and Neocallimastigomycota (0.9%–3.3%). The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum (p < 0.05), indicating that the donkey hindgut region was associated with differences in fungal community composition. Moreover, the relative abundance of enzymes related to plant cell wall degradation were predicted by PICRUSt, and they were also lower in caecum than in colon. The present study provided new information about fibrolytic enzyme profiles and fungal composition in donkey hindgut ecosystem.

Dietary Energy Level Impacts the Performance of Donkeys by Manipulating the Gut Microbiome and Metabolome

Considerable evidence suggests that dietary energy levels and gut microbiota are pivotal for animal health and productivity. However, little information exists about the correlations among dietary energy level, performance, and the gut microbiota and metabolome of donkeys. The objective of this study was to investigate the mechanisms by which dietary energy content dictates the growth performance by modulating the intestinal microbiome and metabolome of donkeys. Thirty-six nine-month-old male Dezhou donkeys with similar body weights were randomly assigned to two groups fed low- or high-energy diets (LE or HE). The results showed that donkeys fed HE had increased (p < 0.05) the average daily gain (ADG) and feed efficiency (G/F) compared with those that received LE diet. The gut microbiota in both groups was dominated by the phyla Firmicutes and Bacteroidetes regardless of the dietary energy level. However, feeding HE to donkeys significantly decreased (p < 0.05) the ratio of Firmicutes to Bacteroidetes (F/B). Compared to the LE group, feeding HE specifically increased the abundances of unidentified_Prevotellaceae (p = 0.02) while decreasing the richness of unidentified_Ruminococcaceae (p = 0.05). Compared to the LE group, feeding the HE diet significantly (p < 0.05) upregulated certain metabolic pathways involving the aspartate metabolism and the urea cycle. In addition, the increased bacteria and metabolites in the HE-fed group exhibited a positive correlation with improved growth performance of donkeys. Taken together, feeding the HE diet increased the richness of Prevotellaceae and upregulated growth-related metabolic pathways, which may have contributed to the ameliorated growth performance of donkeys. Thus, it is a recommendable dietary strategy to feed HE diets to fattening donkeys for superior product performance and feed efficiency.

Transport stress affects the fecal microbiota in healthy donkeys

Background

With the development of large‐scale donkey farming in China, long‐distance transportation has become common practice, and the incidence of intestinal diseases after transportation has increased. The intestinal microbiota is important in health and disease, and whether or not transportation disturbs the intestinal microbiota in donkeys has not been investigated.

Objectives

To determine the effects of transportation on the fecal microbiota of healthy donkeys using 16S rRNA sequencing.

Animals

Fecal and blood samples were collected from 12 Dezhou donkeys before and after transportation.

Methods

Prospective controlled study. Cortisol, ACTH, and heat‐shock protein 90 (HSP90) concentrations were measured. Sequencing of 16S rRNA was used to assess the microbial composition. Alpha diversity and beta diversity were assessed.

Results

Results showed significant (P < .05) increases in cortisol (58.1 ± 14.6 to 71.1 ± 9.60 ng/mL), ACTH (163.8 ± 31.9 to 315.8 ± 27.9 pg/mL), and HSP90 (10.8 ± 1.67 to 14.6 ± 1.75 ng/mL) on the day of arrival. A significantly lower (P = .04) level of bacterial richness was found in fecal samples after transportation, compared with that before transportation without distinct changes in diversity. Most notably, donkeys had significant decreases in Atopostipes, Eubacterium, Streptococcus, and Coriobacteriaceae.

Conclusions and Clinical Importance

Transportation can induce stress in healthy donkeys and have some effect on the composition of the in fecal microbiota. Additional studies are required to understand the potential effect of these microbiota changes, especially significantly decreased bacteria, on the development intestinal diseases in donkeys during recovery from transportation.

Comparative analysis of fecal microbiota composition diversity in Tibetan piglets suffering from diarrheagenic Escherichia coli (DEC)

This study was ascertained to investigate the adverse effects of pathogenic E. coli on gut microbiota of Tibetan piglets with history of yellow and white dysentery. For this purpose, a total of 18 fecal samples were collected from infected and healthy Tibetan piglets for 16S rRNA gene amplification and sequencing of V3-V4 region. Results showed that Firmicutes, Bacteroidia Fusobacteriota, Proteobacteria and Actinobacteriota were the predominant bacteria in Tibetan piglets at the level of phylum classification. Results on classification at family level showed that Lactobacillus, Bacteroidota, Fusobacteriota and Enterobacteriaceae were the dominant bacteria. Results on classification of bacteria at phylum level compared with normal piglets indicated that Bacteroidota, Actinobacteriota, Euryarchaota and Spirochaetota in fecal microbial community in Tibetan piglets showing yellow dysenteric and diarrhea group were significantly decreased (P ≤ 0.05). Compared with the feces of healthy Tibetan piglets, the abundance of Escherichia-Shigella, Lactobacillus and Enterococcus increased significantly in feces of Tibetan piglets having yellow dysentery and white dysentery. Moreover, results exhibited that the Proteobacteria and Fusobacteriota were significantly increased (P ≤ 0.05) suggesting dominant microbial community. Results revealed that E. coli induced different pathological alterations in intestine including damage to intestinal epithelial cells, infiltration of inflammatory cells, presence of red blood cells in spaces of tissues, hemorrhages and necrosis of intestinal villi in piglets with history of yellow dysentery. This study for the first time reported the composition, characteristics, and differences of the fecal microflora diversity of Tibetan piglets with yellow and white dysentery in Qinghai-Tibet Plateau, which can provide a suitable support for effective control of diarrhoeal disease in these animals.

Comparative Metagenomic Analysis of Chicken Gut Microbial Community, Function, and Resistome to Evaluate Noninvasive and Cecal Sampling Resources

When conducting metagenomic analysis on gut microbiomes, there is no general consensus concerning the mode of sampling: non-contact (feces), noninvasive (rectal swabs), or cecal. This study aimed to determine the feasibility and comparative merits and disadvantages of using fecal samples or rectal swabs as a proxy for the cecal microbiome. Using broiler as a model, gut microbiomes were obtained from cecal, cloacal, and fecal samples and were characterized according to an analysis of the microbial community, function, and resistome. Cecal samples had higher microbial diversity than feces, while the cecum and cloaca exhibited higher levels of microbial community structure similarity compared with fecal samples. Cecal microbiota possessed higher levels of DNA replicative viability than feces, while fecal microbiota were correlated with increased metabolic activity. When feces were excreted, the abundance of antibiotic resistance genes like tet and ErmG decreased, but some antibiotic genes became more prevalent, such as fexA, tetL, and vatE. Interestingly, Lactobacillus was a dominant bacterial genus in feces that led to differences in microbial community structure, metabolism, and resistome. In conclusion, fecal microbiota have limited potential as a proxy in chicken gut microbial community studies. Thus, feces should be used with caution for characterizing gut microbiomes by metagenomic analysis.

Unveiling the Biogeography and Potential Functions of the Intestinal Digesta- and Mucosa-Associated Microbiome of Donkeys

The intestinal microbial composition and metabolic functions under normal physiological conditions in the donkey are crucial for health and production performance. However, compared with other animal species, limited information is currently available regarding the intestinal microbiota of donkeys. In the present study, we characterized the biogeography and potential functions of the intestinal digesta- and mucosa-associated microbiota of different segments of the intestine (jejunum, ileum, cecum, and colon) in the donkey, focusing on the differences in the microbial communities between the small and large intestine. Our results show that, Firmicutes and Bacteroidetes dominate in both the digesta- and mucosa-associated microbiota in different intestinal locations of the donkey. Starch-degrading and acid-producing (butyrate and lactate) microbiota, such as Lactobacillus and Sarcina, were more enriched in the small intestine, while the fiber- and mucin-degrading bacteria, such as Akkermansia, were more enriched in the large intestine. Furthermore, metabolic functions in membrane transport and lipid metabolism were more enriched in the small intestine, while functions for energy metabolism, metabolism of cofactors and vitamins, amino acid metabolism were more enriched in the large intestine. In addition, the microbial composition and functions in the digesta-associated microbiota among intestinal locations differed greatly, while the mucosal differences were smaller, suggesting a more stable and consistent role in the different intestinal locations. This study provides us with new information on the microbial differences between the small and large intestines of the donkey and the synergistic effects of the intestinal microbiota with host functions, which may improve our understanding the evolution of the equine digestive system and contribute to the healthy and efficient breeding of donkeys.

The Composition and Predictive Function of the Fecal Microbiota Differ Between Young and Adult Donkeys

The community of microorganisms inhabiting the gastrointestinal tract of monogastric herbivores played critical roles in the absorption of nutrients and keeping the host healthy. However, its establishment at different age groups has not been quantitatively and functionally examined. The knowledge of microbial colonization and its function in the intestinal tract of different-age donkeys is still limited. By applying the V3–V4 region of the bacterial 16S rRNA gene and functional prediction on fecal samples from different-age donkeys, we characterized the gut microbiota during the different age groups. In contrast to the adult donkeys, the gut microbiota diversity and richness of the young donkeys showed significantly less resemblance. The microbial data showed that diversity and richness increased with age, but a highly individual variation of microbial composition was observed at month 1. Principal coordinate analysis (PCoA) revealed a significant difference across five time points in the feces. The abundance of Bacteroides, Lactobacillus, and Odoribacter tended to decrease, while the proportion of Streptococcus was significantly increased with age. For functional prediction, the relative abundance of pathways had a significant difference in the feces across different age groups, for example, Terpenoids and Polyketides and Folding, Sorting, and Degradation (P < 0.05 or P < 0.01). The analysis of beta diversity (PCoA and LEfSe) and microbial functions predicted with PICRUSt (NSTIs) clearly divided the donkeys into foals (≤3 months old) and adults (≥7 months old). Microbial community composition and structure had distinctive features at each age group, in accordance with functional stability of the microbiota. Our findings established a framework for understanding the composition and function of the fecal microbiota to differ between young and adult donkeys.

Comparison of In Vivo and In Vitro Digestibility in Donkeys

We compared in vivo and in vitro dry matter (DM) and neutral detergent fiber (NDF) digestibility in donkeys using feces as microbial inoculum. Four donkeys were used in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments. The animals were fed two types of hay, with or without flaked barley. For the in vivo procedure, total feces were collected for 6 days from each donkey; digestibility was calculated as the difference between ingested and excreted DM and NDF. For the in vitro procedure, donkey feces were buffered and used as microbial inoculum in an Ankom DaisyII Incubator; digestibility was estimated after 60 h of incubation. In vivo results showed that the addition of barley to hays did not change the digestibility values. In vivo estimates were higher than in vitro ones. The equations used to predict in vivo estimates from in vitro data were not reliable (R2 = 0.47 and 0.21; P = 0.003 and 0.078 for NDF and DM digestibility, respectively). Further studies need to evaluate different sample size and digestion times.

Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments of Mongolian horses

The intestinal microbiota plays an important role in the health and metabolism of the host. Next‐generation sequencing technology has enabled the characterization of the gut microbiota of several animal species. We analyzed the intestinal microbiota in six different parts of the gastrointestinal tracts (GITs) of five Mongolian horses by sequencing the 16S rRNA gene V3‐V4 hypervariable region. All horses were kept in the natural habitat of the Inner Mongolia grassland. Significant differences were observed among the microbiota compositions of the distinct GIT regions. In addition, while the microbial community structures of the small and large intestine were significantly different, those of the cecum and colon were similar. In the foregut, Firmicutes (65%) and Proteobacteria (23%) were the most abundant, while Firmicutes (45%) and Bacteroidetes (42%) were the most common in the hindgut. At the level of family, Ruminococcaceae (p = .203), Lachnospiraceae (p = .157), Rikenellaceae (p = .122), and Prevotellaceae (p = .068) were predominant in the hindgut, while the relative abundance of the Akkermansia genus (5.7%, p = .039) was higher in the ventral colon. In terms of the putative functions, the ratio of microbial abundance in the different parts of the GIT was similar, the result can help characterize the gut microbial structure of different animals.