Animal microbiome最新文献

Fecal microbiota transplantation (FMT) is gaining attention as a method to modulate the gut microbiome in pigs, with the goal of enhancing health and production outcomes. While some studies indicate that FMT can enhance growth performance and intestinal health in piglets, others report minimal or even negative effects. This variability highlights the need for standardized protocols and further research to optimize FMT for swine applications. Currently, the use of FMT in pigs is still in its early stages, with limited studies showing considerable methodological differences. Although some evidence supports the effectiveness of FMT, significant gaps remain in our understanding of its approach and underlying mechanisms. Therefore, this review summarizes the role and development of gut microbiota in pigs, analyzes existing FMT research in pigs, emphasizes the varying outcomes, illustrates the potential mechanisms of action based on human and animal studies and discusses the innovative potential of using co-evolved microbial communities as a transplant material. As our understanding of pig gut microbiome advances, FMT and related microbiome-based interventions could become valuable tools in pig production. However, ongoing research is essential to elucidate their mechanisms and develop reliable protocols.

The growing global population and rising living standards require a higher supply of dairy products. Dairy cows are the most important source of milk production, with billions of microorganisms present in the rumen. This study aims to assess the impact of direct-fed microbials (DFMs) containing Lentilactobacillus buchneri, Bifidobacterium longum, and Pediococcus pentosaceus on rumen fermentation parameters, rumen microbial composition, and lactation performance in dairy cows. Twelve Sanhe dairy cows with similar physical condition, parity and lactation were randomly divided into two groups of six cows each. The control group was fed a basal diet and the treatment group was fed a basal diet plus DFMs (20 g/day) for the experimental period of 60 days. Rumen fluid, blood, milk, and feces were collected from cows for detection and analysis. DFMs enhanced the apparent total tract digestibility of crude protein and neutral detergent fiber (P < 0.05), and elevated milk protein rate of Sanhe dairy cows (P < 0.05). In the ruminal environment, supplementation of DFMs promoted the production of microbial proteins, acetate and total volatile fatty acids (P < 0.05). High-throughput sequencing analysis of rumen microorganisms revealed that relative abundance of DFMs were elevated in the treatment group, and DFMs enhanced the relative abundance of Prevotella, Pseudoclostridium and Faecalibacterium in the rumen (P < 0.05). In predictive analysis of microbial functional genes, the treatment group was enriched with more genes encoding hemicellulose-degrading enzymes such as GH10, GH30, and GH67, while the relative abundance of genes encoding enzymes that metabolize ammonia was increased. In addition, the analysis of rumen bacteriophages showed that DFMs significantly increased the relative abundance of bacteriophages infecting Prevotella in the rumen. Overall, DFMs enhanced the degradation of protein and carbohydrate in Sanhe dairy cows. There was a positive correlation with the relative abundance of Prevotella, which may provide substant amino acids and energy for milk protein synthesis, improving the lactation performance of Sanhe dairy cows.

Background: Using probiotics as a substitute for antibiotic growth promoters and reducing odor has received increasing attention in animal science. Despite the extensive investigation into the effects of probiotic administration on swine growth performance and odor reduction by short study durations, the analysis of carcass characteristics and potential mechanistic insights involving gut microbiota and downstream pathways is still few.

Methods: A total of 48 crossbred LYD [(Landrace x Yorkshire) x Duroc] piglets (equal numbers of males and females) were randomly assigned to one of four dietary treatments: control (CON), Lactobacillus kefiranofaciens M1 (M1), M1 + Bacillus amyloliquefaciens S20 (SA group) and M1 + S20 + Bacillus subtilis S14 (SAM group). During the nursery phase (4-8 weeks), pigs were pair-housed and monitored for diarrhea. From 8 to 19 weeks of age, pigs were individually housed and fed grower-finisher diets. Growth performance, blood biochemistry, fecal enzyme activity, and odor-related metabolites were assessed at multiple time points. At market weight (~ 110 kg), six pigs per group were slaughtered for carcass and cecal microbiota analysis.

Results: The results demonstrated that administration of the probiotics led to increased body weight and average daily weight gain, particularly notable during the weaning and finishing periods. Additionally, the SA and SAM groups significantly reduced skatole concentration in feces. Furthermore, probiotic supplementation was associated with increased carcass weight, with the SAM group exhibiting significantly higher tenderloin weight than the CON group. Microbiota analysis revealed taxa exhibiting significant differences in abundance among groups, with corresponding LEfSe findings.

Conclusion: Administering Bacillus subtilis S14 and B. amyloliquefaciens S20 (SA group) impacted growth performance, reduced fecal odor, and enhanced pig carcass quality. The identified probiotic strains hold promise as feed additives, offering a potential solution to challenges encountered by the swine industry.

Background: The skin surfaces of fish harbour diverse assemblages of microbes (microbiomes) that play critical roles in host health and disruption of these microbiomes can lead to disease conditions. Antibiotics, widely used in medicine for human and animal health treatments, are increasingly found in waterways and this is a growing concern due to their potential to alter the balance of microbial ecosystems and drive antimicrobial resistance (AMR). The effects of antibiotics on skin microbiomes in fish, however, have been little explored. This study examines how exposure to environmental levels of antibiotics affects the skin microbiomes of Eurasian carp (Cyprinus carpio).

Results: A 2-week exposure of Eurasian carp to cocktails of five antibiotics (ciprofloxacin, clarithromycin, sulfamethoxazole, trimethoprim, and tetracycline) at concentrations found in the environment resulted in significant skin bacterial community compositional shifts. Applying 16S rRNA amplicon sequencing, we found enrichment of the genus Arcicella (Proteobacteria) and depletion of Sphaerotilus (Bacteroidetes) with limited recovery even after maintaining the fish for a further two weeks in clean (antibiotic-free) water. In the low-antibiotic concentration exposure group, the tank water microbiome assemblages resembled those of the fish skin suggesting similar responses to the antibiotic treatments. Metagenomic analysis observed no increase in antibiotic resistance genes or changes in metabolic pathway abundance, possibly due to the relatively short duration of antibiotic exposure.

Conclusion: This study highlights that even low-level exposure to chemical mixtures can alter fish skin microbiome compositions, with limited recovery observed after cessation of exposure. These findings warrant further assessments of the long-term effects and functional consequences of these altered microbiomes on fish health, particularly in environments increasingly affected by anthropogenic chemical pollution.

Background: The aim of this study was to elucidate the dynamic characteristics of the Taihe Silky Fowl (TSF) intestinal microbiota systematically and predict their biological functions from hatching to market through large-scale sampling and 16S rRNA gene sequencing of a total of 288 samples taken at 8 timepoints from 3 intestinal regions to provide a theoretical basis for optimizing the intestinal microbiota to promote growth performance and intestinal health through artificial interventions on the basis of different growth ages and intestinal regions.

Results: The alpha and beta diversity of the intestinal microbiota changed significantly with age in different intestinal regions. In terms of alpha diversity, the ACE index and Shannon index followed the order cecum > rectum > duodenum, while the Simpson index followed the order rectum and duodenum > cecum. The PCoA plots revealed significant differences in beta diversity at different ages and in intestinal regions. The core phyla (top 5) in the TSF microbiota were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Cyanobacteria. The core genera (top 10) were Lactobacillus, Bacillus, Escherichia-Shigella, Alistipes, norank_o__Clostridia_UCG-014, Bacteroides, Faecalibacterium, norank_f__Ruminococcaceae, Enterococcus and Streptococcus. Additionally, the degree centrality of the cecal microbiota rapidly increased from hatching to 1 week of age, then rapidly decreased from 1 to 2 weeks of age, where it remained relatively stable until 21 weeks of age, whereas the betweenness centrality exhibited the opposite trend; the closeness centrality decreased continuously with age. The functions of the cecal microbiota varied at different ages, and the central functions were nucleic acid metabolism and protein synthesis at 0 weeks of age and carbohydrate metabolism and quorum sensing at 9 weeks of age.

Conclusions: In conclusion, the diversity, structure, composition, community relationships and functions of the intestinal microbiota in Taihe Silky Fowl dynamically changed with age in different intestinal regions.

Zinc is an important trace element for animal health and physiology, and it is routinely provided as a supplement in livestock diets. High levels of dietary zinc have been found to be beneficial for weanling pigs in preventing diarrhea and improving growth. It has also been associated with better reproductive performance in gestating sows and survival of neonatal piglets. However, little is known about zinc's effect on the microbiome of the gestating sow and her neonatal piglets. Even less is known about its effects on the sow and piglet resistome, which is important because dietary zinc can co-select for antimicrobial resistance. The goal of this randomized controlled dietary feeding trial was to assess the effect of high levels of dietary zinc in the last week of gestation on the microbiomes and resistomes of the gestating sow and her neonatal piglets. Seventy-three gestating sows were randomized to receive a diet with standard zinc levels (125 ppm) or high zinc levels (2500 ppm) approximately one week prior to their anticipated farrowing date. Fecal samples were collected from sows at enrollment and at farrowing and from piglets within 3 days of parturition. Fecal samples underwent 16sS rRNA gene sequencing, and a subset of samples underwent shotgun metagenomic sequencing. Statistically significant differences in richness, diversity and taxonomic composition were observed over time, and sows in the treatment group had significantly higher alpha diversity at farrowing (p = 0.04) and significantly altered levels of 3 taxa (Turicibacter, unclassified Clostridiaceae, and unclassified Christensenellaceae). Several antimicrobial resistance genes were significantly more abundant in the zinc group at farrowing compared to the control group, including tetracycline resistance genes [tet(O); tet(W); tet(32); tet(O/W)]; aminoglycoside resistance genes (APH(3')-IIIa), macrolide-lincosamide-streptogramin (MLS) resistance genes (lsaB; macB); and others (kdpE, Pseudomonas aeruginosa CpxR). No significant differences were observed in the piglet microbiomes or resistomes across sow treatment groups. Overall, high levels of dietary zinc had modest effects on the sow microbiome during the feeding trial. Increases in antimicrobial resistance genes in zinc supplemented sows suggest that supranutritional levels of dietary zinc should be avoided in gestating sows.

Background: Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While high-throughput sequencing is commonly used to characterize bacterial communities in animal microbiota, these methods are less often applied to gut eukaryotic composition. Here we used shotgun metagenomic sequencing to characterize eukaryotic diversity in the microbiomes of wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, sequencing depth, and season of sample collection.

Results: We analyzed a total of 75 fecal samples collected in 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of all samples, respectively (percentages indicate the percent of samples in which each kingdom was observed). Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effects of season, host age, or host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples).

Conclusions: Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is important for primate health monitoring and management strategies.

Background: Florfenicol is a broad-spectrum antimicrobial approved in many countries for treating bacterial infections in production animals. Although florfenicol has been widely used in the US catfish industry, its impact on the native microbiota within catfish tissues remains largely unknown. Florfenicol treatment is followed by a mandatory withdrawal period to ensure drug residues fall below regulatory limits before harvest. This interval also allows for the potential recovery of the native microbiota. In particular, the skin and gill microbiota have often been overlooked in aquaculture microbiome research. Moreover, the dynamics of microbial communities and resistome profiles following drug withdrawal are still poorly understood, despite their ecological significance.

Results: A significant increase in intestinal microbial diversity was observed at the end of the withdrawal period. The highest alpha diversity (Shannon index) was observed in catfish intestines. This increase indicated the restoration of the normal microbiota in catfish intestine. The predominant bacterial phyla shared among catfish gill, intestine, and skin are Proteobacteria (62%), Bacteroidetes (18%), Actinobacteriota (12%), Firmicutes (3%), Patescibacteria (2%), and Verrucomicrobiota (1%). Florfenicol application can have lasting effects through the withdrawal period, particularly altering the intestinal microbial community.

Conclusion: The result of this study underscores the impact of florfenicol treatment on the bacterial landscape and antibiotic resistance in catfish, highlighting significant changes in microbial composition in the catfish intestine and at the end of the withdrawal period. These findings address the need for monitoring and managing antibiotic resistance in fish farming environments.

Introduction: The widespread use of antimicrobials in the livestock industry has raised global concerns regarding the emergence and spread of antimicrobial resistance genes (ARGs). Comprehensive databases of ARGs specific to different farm animal species can greatly improve the surveillance of ARGs within the agri-food sector and beyond. In particular, defining the association of ARGs with mobile genetic elements (MGEs)-the primary agents responsible for the spread and acquisition of resistant phenotypes among bacterial populations-could help assess the transmissibility potential of clinically relevant ARGs. Recognizing the gut microbiota as a vast reservoir of ARGs, we aimed to generate a representative isolate collection and genome database of the swine gut microbiome, enabling high-resolution characterization of ARGs in relation to bacterial host range and their association with MGEs.

Results: We generated a biobank of bacteria from different sections of the gastrointestinal tracts of four clinically healthy pigs housed at a research farm in Ontario, Canada. The culturing was performed under anaerobic conditions using both selective and general enrichment media to ensure the capture of a diverse range of bacterial families within the swine gut microbiota. We sequenced the genomes of 129 unique isolates encompassing 44 genera and 25 distinct families of the swine gut microbiome. Approximately 85.3% (110 isolates) contained one or more ARGs, with a total of 246 ARGs identified across 38 resistance gene families. Tetracycline and macrolide resistance genes were the most prevalent across different lineages of the swine gut microbiota. Additionally, we observed a wide range of MGEs, including integrative conjugative elements, plasmids, and phages, frequently associated with ARGs, indicating that the swine gut ecosystem is conducive to the horizontal transfer of ARGs. High-throughput alignment of the identified ARG-MGE complexes to large-scale metagenomics datasets of the swine gut microbiome suggests the presence of highly prevalent and conserved resistome sequences across diverse pig populations.

Conclusion: Our findings reveal a highly diverse and relatively conserved reservoir of ARGs and MGEs within the gut microbiome of pigs. A deeper understanding of the microbial host range and potential transmissibility of prevalent ARGs in the swine microbiome can inform development of targeted antimicrobial resistance surveillance and disease control programs.