Microbiome Analysis Reveals the Dynamic Alternations in Gut Microbiota of Diarrheal Giraffa camelopardalis

Comparative study of the gut microbiota in three captive Rhinopithecus species

BACKGROUND

Snub-nosed monkeys are highly endangered primates and their population continues to decline with the habitat fragmentation. Artificial feeding and breeding is an important auxiliary conservation strategy. Studies have shown that changes and imbalances in the gut microbiota often cause gastrointestinal problems in captive snub-nosed monkeys. Here, we compare the gut microbiota composition, diversity, and predicted metabolic function of three endangered species of snub-nosed monkeys (Rhinopithecus bieti, R. brelichi, and R. roxellana) under the same captive conditions to further our understanding of the microbiota of these endangered primates and inform captive conservation strategies. 16 S rRNA gene sequencing was performed on fecal samples from 15 individuals (R. bieti N = 5, R. brelichi N = 5, R. roxellana N = 5).

RESULTS

The results showed that the three Rhinopithecus species shared 24.70% of their amplicon sequence variants (ASVs), indicating that the composition of the gut microbiota varied among the three Rhinopithecus species. The phyla Firmicutes and Bacteroidetes represented 69.74% and 18.45% of the core microbiota. In particular, analysis of microbiota diversity and predicted metabolic function revealed a profound impact of host species on the gut microbiota. At the genus level, significant enrichment of cellulolytic genera including Rikenellaceae RC9 gut group, Ruminococcus, Christensenellaceae R7 group, UCG 004 from Erysipelatoclostridiaceae, and UCG 002 and UCG 005 from Oscillospiraceae, and carbohydrate metabolism including propionate and butyrate metabolic pathways in the gut of R. bieti indicated that R. bieti potentially has a stronger ability to use plant fibers as energy substances. Bacteroides, unclassified Muribaculaceae, Treponema, and unclassified Eubacterium coprostanoligenes group were significantly enriched in R. brelichi. Prevotella 9, unclassified Lachnospiraceae, and unclassified UCG 010 from Oscillospirales UCG 010 were significantly enriched in R. roxellana. Among the predicted secondary metabolic pathways, the glycan biosynthesis and metabolism had significantly higher relative abundance in the gut of R. brelichi and R. roxellana than in the gut of R. bieti. The above results suggest that different Rhinopithecus species may have different strategies for carbohydrate metabolism. The Principal coordinate analysis (PCoA) and Unweighted pair-group method with arithmetic mean (UPGMA) clustering tree revealed fewer differences between the gut microbiota of R. brelichi and R. roxellana. Correspondingly, no differences were detected in the relative abundances of functional genes between the two Rhinopithecus species.

CONCLUSION

Taken together, the study highlights that host species have an effect on the composition and function of the gut microbiota of snub-nosed monkeys. Therefore, the host species should be considered when developing nutritional strategies and investigating the effects of niche on the gut microbiota of snub-nosed monkeys.

Intestinal Ecology Changes in Diarrheic Père David's Deer Revealed by Gut Microbiota and Fecal Metabolites Analysis

Diarrhea is one of the most common diseases affecting the health of Père David's deer (Elaphurus davidianus). It is believed that an imbalanced intestinal ecology contributes to the etiology of the condition. However, little is known about how the intestinal ecology changes in these diarrheic animals. In this study, 16S rRNA gene sequencing and ultra-high performance liquid chromatography combined with tandem mass spectrometry (UPLC-MS/MS) were used to investigate the gut microbiota and fecal metabolites in five Père David's deer with diarrhea. The results showed that when compared with healthy individuals, considerable changes in the gut microbiome were observed in diarrheic animals, including a significant reduction in microbial diversity and gut microbiota composition alterations. Furthermore, the profiles of numerous fecal metabolites were altered in diarrheic individuals, showing large-scale metabolite dysregulation. Among metabolites, acylcarnitines, lysophosphatidylcholine, bile acids, and oxidized lipids were elevated significantly. Constantly, several metabolic pathways were significantly altered. Interestingly, predicted metabolic pathways based on 16S rRNA gene sequence and differential metabolite analysis showed that lipid metabolism, cofactor, and vitamin metabolism were altered in sick animals, indicating microbiota-host crosstalk in these deer. When combined, the results provide the first comprehensive description of an intestinal microbiome and metabolic imbalance in diarrheic Père David's deer, which advances our understanding and potential future treatment of diarrheic animals.

Dynamic changes of gut fungal community in horse at different health states

Accumulating studies indicated that gut microbial changes played key roles in the progression of multiple diseases, which seriously threaten the host health. Gut microbial dysbiosis is closely associated with the development of diarrhea, but gut microbial composition and variability in diarrheic horses have not been well characterized. Here, we investigated gut fungal compositions and changes in healthy and diarrheic horses using amplicon sequencing. Results indicated that the alpha and beta diversities of gut fungal community in diarrheal horses changed significantly, accompanied by distinct changes in taxonomic compositions. The types of main fungal phyla (Neocallimastigomycota, Ascomycota, and Basidiomycota) in healthy and diarrheal horses were same but different in relative abundances. However, the species and abundances of dominant fungal genera in diarrheal horses changed significantly compared with healthy horses. Results of Metastats analysis indicated that all differential fungal phyla (Blastocladiomycota, Kickxellomycota, Rozellomycota, Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Neocallimastigomycota, Glomeromycota, and Olpidiomycota) showed a decreasing trend during diarrhea. Moreover, a total of 175 differential fungal genera were identified for the gut fungal community between healthy and diarrheal horses, where 4 fungal genera increased significantly, 171 bacterial genera decreased dramatically during diarrhea. Among these decreased bacteria, 74 fungal genera even completely disappeared from the intestine. Moreover, this is the first comparative analysis of equine gut fungal community in different health states, which is beneficial to understand the important role of gut fungal community in equine health.

Characterization of gut microbiota dysbiosis of diarrheic adult yaks through 16S rRNA gene sequences

The ruminant gut microbial community has a strong impact on host health and can be altered during diarrhea disease. As an indigenous breed of the Tibetan Plateau, domestic yak displays a high diarrhea rate, but little research has been done to characterize the bacterial microbial structure in diarrheic yaks. In the present study, a total of 30 adult yaks, assigned to diarrhea (case, N = 15) and healthy (control, N = 15) groups, were subjected to gut microbiota profiling using the V3–V4 regions of the 16S rRNA gene. The results showed that the gut microbiome of the case group had a significant decrease in alpha diversity. Additionally, differences in beta diversity were consistently observed for the case and control groups, indicating that the microbial community structure was changed due to diarrhea. Bacterial taxonomic analysis indicated that the Bacteroidetes, Firmicutes, and Proteobacteria were the three most dominant phyla in both groups but different in relative abundance. Especially, the proportion of Proteobacteria in the case group was increased as compared with the control group, whereas Spirochaetota and Firmicutes were significantly decreased. At the genus level, the relative abundance of Escherichia-Shigella and Prevotellaceae_UCG-003 were dramatically increased, whereas that of Treponema, p-2534-18B5_gut_group, and Prevotellaceae_UCG-001 were observably decreased with the effect of diarrhea. Furthermore, based on our linear discriminant analysis (LDA) effect size (LEfSe) results, Alistipes, Solibacillus, Bacteroides, Prevotellaceae_UCG_003, and Bacillus were significantly enriched in the case group, while the other five genera, such as Alloprevotella, RF39, Muribaculaceae, Treponema, and Enterococcus, were the most preponderant in the control group. In conclusion, alterations in gut microbiota community composition were associated with yak diarrhea, differentially represented bacterial species enriched in case animals providing a theoretical basis for establishing a prevention and treatment system for yak diarrhea.

Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris)

The gut microbiota has key physiological functions in host adaptation, although little is known about the seasonal changes in the composition and diversity of the gut microbiota in deer. In this study, seasonal variations (grassy and withering season) in the gut microbiota of white-lipped deer (Cervus albirostris), which lives in alpine environments, were explored through 16S rRNA high-throughput sequencing based on sixteen fecal samples collected from Gansu Qilian Mountain National Nature Reserve in China. At the phylum level, Firmicutes, Bacteroidota, and Actinobacteriota dominated the grassy season, while Firmicutes, Proteobacteria, and Actinobacteriota dominated the withering season. At the genus level, Carnobacterium dominated the grassy season, while Arthrobacter and Acinetobacter dominated the withering season. Alpha diversity results (Shannon: P = 0.01, ACE: P = 0.00, Chao1: P = 0.00) indicated that there was a difference in the diversity and richness of the gut microbiota between the two seasons, with higher diversity in the grassy season than in the withering season. Beta diversity results further indicated that there was a significant difference in the community structure between the two seasons (P = 0.001). In summary, the composition, diversity, and community structure of the gut microbiota showed significant seasonal variations, which could be explained by variations in the seasonal food availability, composition, diversity, and nutrition due to phenological alternations. The results of this study indicate that the gut microbiota can adapt to changes in the environment and provide the scientific basis for health assessment of white-lipped deer.

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

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

Comparative Analysis of Gut Microbiota Between Healthy and Diarrheic Horses

Increasing evidence reveals the importance of gut microbiota in animals for regulating intestinal homeostasis, metabolism, and host health. The gut microbial community has been reported to be closely related to many diseases, but information regarding diarrheic influence on gut microbiota in horses remains scarce. This study investigated and compared gut microbial changes in horses during diarrhea. The results showed that the alpha diversity of gut microbiota in diarrheic horses decreased observably, accompanied by obvious shifts in taxonomic compositions. The dominant bacterial phyla (Firmicutes, Bacteroidetes, Spirochaetes, and Kiritimatiellaeota) and genera (uncultured_bacterium_f_Lachnospiraceae, uncultured_bacterium_f_p-251-o5, Lachnospiraceae_AC2044_group, and Treponema_2) in the healthy and diarrheic horses were same regardless of health status but different in abundances. Compared with the healthy horses, the relative abundances of Planctomycetes, Tenericutes, Firmicutes, Patescibacteria, and Proteobacteria in the diarrheic horses were observably decreased, whereas Bacteroidetes, Verrucomicrobia, and Fibrobacteres were dramatically increased. Moreover, diarrhea also resulted in a significant reduction in the proportions of 31 genera and a significant increase in the proportions of 14 genera. Taken together, this study demonstrated that the gut bacterial diversity and abundance of horses changed significantly during diarrhea. Additionally, these findings also demonstrated that the dysbiosis of gut microbiota may be an important driving factor of diarrhea in horses.