Comparative Analyses of the Gut Microbiome of Two Fox Species, the Red Fox (Vulpes Vulpes) and Corsac Fox (Vulpes Corsac), that Occupy Different Ecological Niches

Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome

Species in the family Canidae occupy different spatial ecological niches, and some (e.g., wolf) can be kept in zoos. The gut microbiome may differ among various wild and captive canids. Therefore, we compared the gut microbiomes of wild canids (wolf, red fox, and corsac fox) in the Hulun Lake area, captive wolves, and domestic dogs in different regions using metagenomic data. A random forest analysis revealed significant enrichment for bacterial species producing short-chain fatty acids and the thermogenesis pathway (ko04714) in the gut microbiome of wild wolf, potentially providing sufficient energy for adaptation to a wide range of spatial ecological niches. The significantly enriched bacterial species and functional pathways in the gut microbiome of corsac foxes were related to physiological stability and adaptation to arid environments. Alpha diversity of carbohydrate-active enzymes in the gut microbiome was higher in the red fox than in the corsac fox and wild wolf, which may be related to the abundance of plant seeds (containing carbohydrates) in their diets (red foxes inhabit seed-rich willow bosk habitats). However, the influence of host genetic factors cannot be excluded, and further experimental studies are needed to verify the study results. In addition, captive environments drove similarity in carbohydrate-active enzymes (CAZymes) and virulence factors (VFs) in the gut microbiomes of captive wolf and domestic dog, and increased the diversity of CAZymes and VFs in the gut microbiome of captive wolf. Increased VFs diversity may increase the pathogenic potential of the gut microbiome in captive wolves. Therefore, it is necessary to continue monitoring the health status of captive wolves and develop appropriate management strategies.

Integrated multi-omics reveals the Bacillus amyloliquefaciens BA40 against Clostridium perfringens infection in weaned piglets

INTRODUCTION

Clostridium perfringens (C. perfringens) can cause necrotic enteritis and higher mortality rates in piglets, by impairing the intestinal barrier function. Bacillus amyloliquefaciens 40 (BA40) has showed potential ability to reduce C. perfringens infections, but the mechanisms responsible for its effectiveness remain unclear.

OBJECTIVES

This study aims to evaluate the impact of BA40 on inflammation induced by C. perfringens and to explain the mechanisms underlying its therapeutic effects. We aim to show how BA40 can bolster piglet health by strengthening the intestinal barrier and regulating immune responses.

METHODS

We used piglets and cellular models, alongside microbiomics, metabolomic, and transcriptomic analyses, to investigate BA40's impact on C. perfringens-induced inflammation. A model of C. perfringens infection was constructed using piglets and cells to investigate the effect of BA40 on its phenotype. Microbiomics, metabolomics, and transcriptomics analyses were subsequently used to investigate the mechanisms of protection and immune response to BA40 on the intestinal barrier of piglets.

RESULTS

Our study revealed significant improvements in piglet health following BA40 administration. Notably, BA40 strengthened the intestinal mucosal barrier and mitigated the inflammatory response triggered by C. perfringens BA40 decreased harmful bacteria and increased beneficial bacteria. Metabolite profiles improved, showing a reduction in harmful substances. Transscriptomics analysis indicated BA40's role in TNF/NF-κB signaling pathway, hinting at its ability to regulate immune responses and reduce intestinal inflammation. Cellular assays further confirmed BA40's capacity to diminish inflammatory cytokine release and encourage the differentiation of anti-inflammatory macrophages.

CONCLUSION

Datasets from the present study demonstrate that BA40 modulates gut microbes and metabolites, inhibits inflammation-related signaling pathways, and maintains gut barrier function. Our findings not only deepen our understanding of the therapeutic capacity of BA40 but also provide a theoretical foundation for the development of probiotics and alternative therapies aimed at improving piglet gut health.

Dietary Taurine Regulation of the Intestinal Microbiome in Chinese Stripe-Necked Turtle (Mauremys sinensis)

Taurine is essential for sustaining the body's physiological equilibrium and is extensively utilized as a dietary supplement and immune system enhancer for aquatic creatures. The gut microbiota serves as a vital health indicator in animals. In this study, our goal was to evaluate the effects of dietary taurine on the gut microbiome of Chinese stripe-necked turtles (Mauremys sinensis). Turtles were evenly divided into three supplementation groups: a control group with no taurine in the diet, a low group with 0.1% taurine, and a high group with 0.4% taurine. High-throughput sequencing was employed to analyze the gut microbiome's composition and structure. The results showed that the impact of taurine supplementation on the α-diversity and β-diversity of the gut microbiome was not statistically significant. At the phylum level, Firmicutes and Bacteroidetes predominated the gut microbiome. At the genus level, three beneficial bacteria, Clostridium_sensu_stricto_13, Pygmaiobacter, and Terrisporobacter showed significant differences under different levels of taurine supplementation and increased in abundance with the supplementation of taurine, while the harmful bacterium Brucella decreased in abundance with the addition of taurine and exhibited significant differences. Furthermore, LEfSe analysis and functional predictions highlighted significant variations in the functional traits of gram-positive intestinal bacteria among the different taurine supplementation levels. These findings imply that dietary taurine may alter the intestinal microbiome structure in Chinese stripe-necked turtles, offering valuable insights for the scientific assessment of taurine's health benefits as a feed additive and potentially guiding the formulation of more informed and healthier feeding practices.

Making sense of sentinels: wildlife as the One Health bridge for environmental antimicrobial resistance surveillance

Antimicrobial resistance (AMR), arising from decades of imprudent anthropogenic use of antimicrobials in healthcare and agriculture, is considered one of the greatest One Health crises facing healthcare globally. Antimicrobial pollutants released from human-associated sources are intensifying resistance evolution in the environment. Due to various ecological factors, wildlife interact with these polluted ecosystems, acquiring resistant bacteria and genes. Although wildlife are recognized reservoirs and disseminators of AMR in the environment, current AMR surveillance systems still primarily focus on clinical and agricultural settings, neglecting this environmental dimension. Wildlife can serve as valuable sentinels of AMR in the environment, reflecting ecosystem health, and the effectiveness of mitigation strategies. This review explores knowledge gaps surrounding the ecological factors influencing AMR acquisition and dissemination in wildlife, and highlights limitations in current surveillance systems and policy instruments that do not sufficiently address the environmental component of AMR. We discuss the underutilized opportunity of using wildlife as sentinel species in a holistic, One Health-centred AMR surveillance system. By better integrating wildlife into systematic AMR surveillance and policy, and leveraging advances in high-throughput technologies, we can track and predict resistance evolution, assess the ecological impacts, and better understand the complex dynamics of environmental transmission of AMR across ecosystems.

Comparative analysis of gut microbiota of Chinese Kunming dog, German Shepherd dog, and Belgian Malinois dog

IMPORTANCE

The composition of the gut microbiota is essential for a dog's health and its adaptation to the environment. Different bacteria can produce the same essential metabolites beneficial to health owing to bacterial functional redundancy in microbial communities.

OBJECTIVE

This study examined the gut bacterial communities of dogs from different breeds, all kept under identical domestication conditions.

METHODS

Noninvasive sampling and 16S rRNA high-throughput sequencing were used to compare the composition and function of the gut microbiota of three dog breeds: the Chinese Kunming dog (CKD), German Shepherd dog (GSD), and Belgian Malinois dog (BMD).

RESULTS

The gut microbiota of the three dog breeds consisted of 257 species across 146 genera, 60 families, 35 orders, 15 classes, and 10 phyla. The dominant bacterial phyla across the three breeds were Firmicutes (57.44%), Fusobacteriota (28.86%), and Bacteroidota (7.63%), while the dominant bacterial genera across the three breeds were Peptostreptococcus (21.08%), Fusobacterium (18.50%), Lactobacillus (12.37%), and Cetobacter (10.29%). Further analysis revealed significant differences in the intestinal flora of the three breeds at the phylum and genus levels. The intestinal flora of BMD was significantly richer than that of CKD and GSD. The functional prediction and Kyoto Encyclopedia of Genes and Genomes analysis showed that the primary functions of the gut microbiota in these breeds were similar, with significant enrichment in various metabolic pathways, including carbohydrate and amino acid metabolism, secondary metabolite biosynthesis, and microbial metabolism in different environments. The intestinal flora of these breeds also played a crucial role in genetic information processing, including transcription, translation, replication, and material transport.

CONCLUSIONS AND RELEVANCE

These results provide novel insights into the intestinal flora of intervention dogs and suggest novel methods to improve their health status, which help increase microbial diversity and normalize metabolite production in diseased dogs.

Dietary change influences the composition of the fecal microbiota in two rescued wild raccoon dogs (Nyctereutes procyonoides)

The gut microbiota of wild animals, influenced by various factors including diet, nutrition, gender, and age, plays a critical role in their health and disease status. This study focuses on raccoon dogs (Nyctereutes procyonoides), a commonly found wild animal, and its gut microbiota composition in response to dietary shifts. The study aimed to compare the fecal bacterial communities and diversity of rescued raccoon dogs fed three different diet types (fish and amphibians, mixed protein with maize, and solely maize) using high-throughput sequencing. Results indicated that the dietary composition significantly influenced the gut microbiota, with notable differences in the abundance of several key phyla and genera. The study identified Firmicutes as the dominant phylum in all diet groups, with notable variations in the relative abundances of Bacteroidota, Proteobacteria, and Verrucomicrobiota. Notably, the group solely fed maize exhibited a significant increase in Proteobacteria, potentially linked to dietary fiber and lignin degradation. The genus-level analysis highlighted significant differences, with Lactobacillus and Bifidobacterium responding to dietary shifts. The genus Akkermansia in Verrucomicrobiota can be identified as a marker for assessing the health of the gut and deserves further investigation. Gender-specific differences in the gut microbiota were observed, highlighting the influence of individual variation. Furthermore, the analysis of bacterial functions suggested a connection between diet and host metabolism, emphasizing the need for further research to understand the complex mechanisms underlying the relationship between dietary composition and gut microbiota in wild animals. These findings provide crucial insights into conservation and rescue efforts for wild animals.

Prevalence of Pentatrichomonas hominis in foxes and raccoon dogs and changes in the gut microbiota of infected female foxes in the Hebei and Henan Provinces in China

Pentatrichomonas hominis (P. hominis) is a zoonotic parasite that affects a wide range of hosts, causing gastrointestinal diseases. The present study aimed to evaluate the prevalence of P. hominis among caged foxes and raccoon dogs and the effect of P. hominis on the gut microbiota in female foxes. A total of 893 fresh fecal samples were collected from the Hebei and Henan Provinces in China. P. hominis was screened based on 18S rRNA gene expression via nested PCR. The difference in the gut microbiota between nine P. hominis-positive and nine P. hominis-negative samples was investigated by 16S rRNA gene sequencing. The total prevalence of P. hominis infection in foxes and raccoon dogs was 31.7% (283/893). The prevalence rates of P. hominis infection were 28.2% (88/312) and 33.6% (195/581) in foxes and raccoon dogs, respectively. Phylogenetic analysis revealed that all P. hominis strains detected in foxes and raccoon dogs in the present study were the zoonotic genotype CC1. Moreover, compared with those in the P. hominis-negative group, the diversity of the gut microbiota in the P. hominis-positive group was lower, and the abundance of Firmicutes and the ratio of Firmicutes/Bacteroidetes (F/B) in the P. hominis-positive group were lower than those in the P. hominis-negative group. We speculate that these differences may be due to indigestion and diarrhea in infected female foxes. Overall, the present study evaluated the prevalence of P. hominis in foxes and raccoon dogs in the Henan and Hebei Provinces and revealed that P. hominis infection interrupted the diversity of the gut microbiota in female foxes.

Metagenomic analysis of gut microbiome and resistome of Whooper and Black Swans: a one health perspective

BACKGROUND

With the promotion of "One Health," the health of animals and their impact on the environment have become major concerns recently. Widely distributed in China, the whooper swans (Cygnus cygnus) and black swans (Cygnus atratus) are not only important to the ecological environment, but they may also potentially influence public health security. The metagenomic approach was adopted to uncover the impacts of the gut microbiota of swans on host and public health.

RESULTS

In this study, the intestinal microbiome and resistome of migratory whooper swans and captive-bred black swans were identified. The results revealed similar gut microbes and functional compositions in whooper and black swans. Interestingly, different bacteria and probiotics were enriched by overwintering whooper swans. We also found that Acinetobacter and Escherichia were significantly enriched in early wintering period swans and that clinically important pathogens were more abundant in black swans. Whooper swans and black swans are potential reservoirs of antibiotic resistance genes (ARGs) and novel ARGs, and the abundance of novel ARGs in whooper swans was significantly higher than that in black swans. Metagenomic assembly-based host tracking revealed that most ARG-carrying contigs originated from Proteobacteria (mainly Gammaproteobacteria).

CONCLUSIONS

The results revealed spatiotemporal changes in microbiome and resistome in swans, providing a reference for safeguarding public health security and preventing animal epidemics.

High-Quality Chromosome-Level Genome Assembly of the Corsac Fox (Vulpes corsac) Reveals Adaptation to Semiarid and Harsh Environments

The Corsac fox (Vulpes corsac) is a species of fox distributed in the arid prairie regions of Central and Northern Asia, with distinct adaptations to dry environments. Here, we applied Oxford-Nanopore sequencing and a chromosome structure capture technique to assemble the first Corsac fox genome, which was then assembled into chromosome fragments. The genome assembly has a total length of 2.2 Gb with a contig N50 of 41.62 Mb and a scaffold N50 of 132.2 Mb over 18 pseudo-chromosomal scaffolds. The genome contained approximately 32.67% of repeat sequences. A total of 20,511 protein-coding genes were predicted, of which 88.9% were functionally annotated. Phylogenetic analyses indicated a close relation to the Red fox (Vulpes vulpes) with an estimated divergence time of ~3.7 million years ago (MYA). We performed separate enrichment analyses of species-unique genes, the expanded and contracted gene families, and positively selected genes. The results suggest an enrichment of pathways related to protein synthesis and response and an evolutionary mechanism by which cells respond to protein denaturation in response to heat stress. The enrichment of pathways related to lipid and glucose metabolism, potentially preventing stress from dehydration, and positive selection of genes related to vision, as well as stress responses in harsh environments, may reveal adaptive evolutionary mechanisms in the Corsac fox under harsh drought conditions. Additional detection of positive selection for genes associated with gustatory receptors may reveal a unique desert diet strategy for the species. This high-quality genome provides a valuable resource for studying mammalian drought adaptation and evolution in the genus Vulpes.

Differences in the luminal and mucosal gut microbiomes and metabolomes of oriental rat snake (Ptyas mucosus)

Previous studies regarding the gastrointestinal biogeography of microbiomes generally focused on longitudinal comparisons, whereas few studies have compared luminal and mucosal microbiomes. Investigations of the snake gut microbiome have attracted interest because of the unique digestive physiology and hibernation behavior, but adequate sampling methods must be developed. Here, we used an omics approach combining 16S rRNA gene sequencing with untargeted metabolomics to profile the luminal and mucosal gut microbiomes and metabolomes in oriental rat snakes, with the goal of revealing the heterogeneity and co-occurrence at these sites. The α-diversity of the gut microbiome was significantly higher at mucosal sites than at luminal sites. Microbial composition also differed according to sampling site, with significant differences in the abundances of dominant phyla and genera, as well as β-diversity clustering and distribution. Metabolome profiling revealed differences that were mainly related to cholinergic substances and nucleic acids. Analysis of variations in Kyoto Encyclopedia of Genes and Genomes functions of microbes and metabolites showed that the mucosal microbiome was more frequently involved in genetic information processing and cellular processes, whereas the luminal microbiome generally participated in metabolic regulation. Notably, we found a greater abundance of the opportunistic pathogen genus Escherichia-Shigella at luminal sites and higher levels of the lipid-regulator metabolite fenfluramine at mucosal sites. Despite the extensive differences between the two sampling sites, the results revealed similarities in terms of amplicon sequence variant composition and dominant core microbes. This pilot exploration of luminal and mucosal microbiomes and metabolites provides key insights to guide future research. KEY POINTS: • Snake luminal and mucosal microbiota was distinct in composition and function. • Metabolome profiling revealed differences related to different metabolites. • The pathogenic microbes are more likely to colonize the gut lumina.

Comparative Analyses of the Fecal Microbiome of Five Wild Black-Billed Capercaillie (Tetrao parvirostris) Flocks

Black-billed capercaillie (Tetrao parvirostris) was listed as a first-class state-protected animal because it was endangered in China (Category I). This study is the first to examine the diversity and composition of T. parvirostris gut microbiome in the wild. We collected fecal samples from five black-billed capercaillie flock roosting sites (each 20 km apart) in one day. Thirty fecal samples were sequenced with 16S rRNA gene amplicons on the Illumina HiSeq platform. This study is the first to analyze the fecal microbiome composition and diversity of black-billed capercaillie in the wild. At the phylum level, Camplyobacterota, Bacillota, Cyanobacteria, Actinomycetota, and Bacteroidota were the most abundant in the fecal microbiome of black-billed capercaillie. At the genus level, unidentified Chloroplast, Escherichia-Shigella, Faecalitalea, Bifidobacterium, and Halomonas were the dominant genera. Based on alpha and beta diversity analyses, we found no significant differences in the fecal microbiome between five flocks of black-billed capercaillie. Protein families: genetic information processing; protein families: signaling and cellular processes, carbohydrate metabolism; protein families: metabolism and energy metabolism are the main predicted functions of the black-billed capercaillie gut microbiome through the PICRUSt2 method. This study reveals the composition and structure of the fecal microbiome of the black-billed capercaillie under wild survival conditions, and this study provides scientific data for the comprehensive conservation of the black-billed capercaillie.

Characteristics of Microbiota in Different Segments of the Digestive Tract of Lycodon rufozonatus

The gastrointestinal tract of animals contains microbiota, forming a complex microecosystem. Gut microbes and their metabolites can regulate the development of host innate and adaptive immune systems. Animal immune systems maintain intestinal symbiotic microbiota homeostasis. However, relatively few studies have been published on reptiles, particularly snakes, and even fewer studies on different parts of the digestive tracts of these animals. Herein, we used 16S rRNA gene sequencing to investigate the microbial community composition and adaptability in the stomach and small and large intestines of Lycodon rufozonatus. Proteobacteria, Bacteroidetes, and Firmicutes were most abundant in the stomach; Fusobacteria in the small intestine; and Proteobacteria, Bacteroidetes, Fusobacteria, and Firmicutes in the large intestine. No dominant genus could be identified in the stomach; however, dominant genera were evident in the small and large intestines. The microbial diversity index was significantly higher in the stomach than in the small and large intestines. Moreover, the influence of the microbial community structure on function was clarified through function prediction. Collectively, the gut microbes in the different segments of the digestive tract revealed the unique features of the L. rufozonatus gut microbiome. Our results provide insights into the co-evolutionary relationship between reptile gut microbiota and their hosts.

Evaluating a potential model to analyze the function of the gut microbiota of the giant panda

To contribute to the conservation of endangered animals, the utilization of model systems is critical to analyze the function of their gut microbiota. In this study, the results of a fecal microbial transplantation (FMT) experiment with germ-free (GF) mice receiving giant panda or horse fecal microbiota showed a clear clustering by donor microbial communities in GF mice, which was consistent with the results of blood metabolites from these mice. At the genus level, FMT re-established approximately 9% of the giant panda donor microbiota in GF mice compared to about 32% for the horse donor microbiota. In line with this, the difference between the panda donor microbiota and panda-mice microbiota on whole-community level was significantly larger than that between the horse donor microbiota and the horse-mice microbiota. These results were consistent with source tracking analysis that found a significantly higher retention rate of the horse donor microbiota (30.9%) than the giant panda donor microbiota (4.0%) in GF mice where the microbiota remained stable after FMT. Further analyzes indicated that the possible reason for the low retention rate of the panda donor microbiota in GF mice was a low relative abundance of Clostridiaceae in the panda donor microbiota. Our results indicate that the donor microbiota has a large effect on GF mice microbiota after FMT.

High Dietary Histamine Induces Digestive Tract Oxidative Damage in Juvenile Striped Catfish (Pangasianodon hypophthalmus)

A 56-day feeding trial investigated the effects of dietary histamine on the antioxidant capacity, gastric and intestinal barrier functions, and growth performance of striped catfish (Pangasianodon hypophthalmus). Seven isonitrogenous (34.0% crude protein) and isolipidic (10.5% crude lipid) diets were formulated with supplemental 0, 15, 30, 60, 120, 240, and 480 mg/kg of histamine, named H0, H15, H30, H60, H120, H240, and H480 group, respectively. Results showed that the weight gain rate, specific growth rate, relative intestinal length in the H240 and H480 groups, and the condition factors in the H480 group were significantly lower than those in the H0 group. Intestinal total antioxidant capacity, peroxidase, catalase, superoxide dismutase, glutathione peroxidase, and glutathione reductase activities in the H480 group were significantly lower than those in the H0 group, whereas intestinal malondialdehyde content exhibited the opposite trend. Intestinal complement 3, complement 4, immunoglobulin M, and Recombinant Mucin 2 in the H480 group were significantly lower than those in the H0 group, in contrast to intestinal lipopolysaccharide content. Intestinal IL-10 gene expression in the H480 group was significantly lower than that in the H0 group, whereas the TNF-α, IL-1, IL-6, and IL-8 gene expression exhibited opposite results. Scanning and transmission electron microscopic observation of the gastrointestinal tract revealed severe damage to the gastric mucosa and intestinal epithelium in the H480 group. The abundance of Treponema in the histamine groups was significantly higher than that in the H0 group. These results indicated that high dietary histamine decreases intestinal immunity and antioxidant capacity, inducing digestive tract oxidative damage and ultimately decreasing the growth of striped catfish.

An overview of bats microbiota and its implication in transmissible diseases

Recent pandemic events have raised the attention of the public on the interactions between human and environment, with particular regard to the more and more feasible transmission to humans of micro-organisms hosted by wild-type species, due to the increasing interspecies contacts originating from human’s activities. Bats, due to their being flying mammals and their increasing promiscuity with humans, have been recognized as hosts frequently capable of transmitting disease-causing microorganisms. Therefore, it is of considerable interest and importance to have a picture as clear as possible of the microorganisms that are hosted by bats. Here we focus on our current knowledge on bats microbiota. We review the most recent literature on this subject, also in view of the bat’s body compartments, their dietary preferences and their habitat. Several pathogenic bacteria, including many carrying multidrug resistance, are indeed common guests of these small mammals, underlining the importance of preserving their habitat, not only to protect them from anthropogenic activities, but also to minimize the spreading of infectious diseases.

High-Altitude Drives the Convergent Evolution of Alpha Diversity and Indicator Microbiota in the Gut Microbiomes of Ungulates

Convergent evolution is an important sector of evolutionary biology. High-altitude environments are one of the extreme environments for animals, especially in the Qinghai Tibet Plateau, driving the inquiry of whether, under broader phylogeny, high-altitude factors drive the convergent evolution of Artiodactyla and Perissodactyla gut microbiomes. Therefore, we profiled the gut microbiome of Artiodactyla and Perissodactyla at high and low altitudes using 16S rRNA gene sequencing. According to cluster analyses, the gut microbiome compositions of high-altitude Artiodactyla and Perissodactyla were not grouped together and were far from those of low-altitude Artiodactyla and Perissodactyla. The Wilcoxon’s test in high-altitude ungulates showed significantly higher Sobs and Shannon indices than in low-altitude ungulates. At the phylum level, Firmicutes and Patescibacteria were significantly enriched in the gut microbiomes of high-altitude ungulates, which also displayed a higher Firmicutes/Bacteroidetes value than low-altitude ungulates. At the family level, Ruminococcaceae, Christensenellaceae, and Saccharimonadaceae were significantly enriched in the gut microbiomes of high-altitude ungulates. Our results also indicated that the OH and FH groups shared two significantly enriched genera, Christensenellaceae_R_7_group and Candidatus_Saccharimonas. These findings indicated that a high altitude cannot surpass the order level to drive the convergent evolution of ungulate gut microbiome composition but can drive the convergent evolution of alpha diversity and indicator microbiota in the gut microbiome of ungulates. Overall, this study provides a novel perspective for understanding the adaptation of ungulates to high-altitude environments.

Analysis and Comparison of Gut Microbiome in Young Detection Dogs

The detection dogs are well-known for their excellent capabilities to sense different kinds of smells, which can play an important role in completing various searching and rescuing missions. The recent studies have demonstrated that the excellent olfactory function of detection dogs might be related with the gut microbes via the bidirectional communications between the gastrointestinal tract and the brain. In this study, the gut microbial communities of three types of breeds of detection dogs (Springer Spaniel, Labrador Retriever, and German Shepherd) were studied and compared. The results revealed that the richness and the diversity of gut microbiome German Shepherd dogs were significantly higher than the Labrador Retriever dogs and the Springer Spaniel dogs. At the phylum level, the most predominant gut microbial communities of the detection dogs were comprised of Fusobacteriota, Bacteroidetes, Firmicutes, Proteobacteria, Campilobacterota, and Actinobacteriota. At the genus level the most predominant gut microbial communities were comprised of Fusobacterium, Megamonas, Prevotella, Alloprevotella, Bacteroides, Haemophilus, Anaerobiospirillum, Helicobacter, Megasphaera, Peptoclostridium, Phascolarctobacterium, and Streptococcus. However, the gut microbial communities of the three dogs group were also obviously different. The mean relative abundance of Fusobacterium, Prevotella, Alloprevotella, Megamonas, Bacteroides, and Phascolarctobacterium presented significant differences in the three groups. According to the portraits and characteristics of the gut microbiome in young detection dogs, multiple kinds of nutritional interventions could be applied to manipulate the gut microbiota, with the aim of improving the health states and the olfactory performances.